Starting phenix.real_space_refine on Thu Oct 29 20:26:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6rdb_4812/10_2026/6rdb_4812.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rdb_4812/10_2026/6rdb_4812.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6rdb_4812/10_2026/6rdb_4812.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rdb_4812/10_2026/6rdb_4812.map" model { file = "/net/cci-nas-00/data/ceres_data/6rdb_4812/10_2026/6rdb_4812.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rdb_4812/10_2026/6rdb_4812.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6rdb_4812/10_2026/6rdb_4812.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6rdb_4812/10_2026/6rdb_4812.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 116 5.16 5 C 21563 2.51 5 N 5800 2.21 5 O 6464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 262 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33961 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "P" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 886 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 5, 'TRANS': 66} Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1303 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain: "S" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2130 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3649 Classifications: {'peptide': 483} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 461} Chain: "U" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3980 Classifications: {'peptide': 523} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain breaks: 1 Chain: "V" Number of atoms: 3961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3961 Classifications: {'peptide': 520} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4115 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 517} Chain: "Y" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3957 Classifications: {'peptide': 521} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 498} Chain: "Z" Number of atoms: 4087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4087 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 513} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "U" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "V" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "X" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "Y" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "Z" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 7.18, per 1000 atoms: 0.21 Number of scatterers: 33961 At special positions: 0 Unit cell: (160.056, 132.678, 207.441, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 116 16.00 P 13 15.00 Mg 5 11.99 O 6464 8.00 N 5800 7.00 C 21563 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 1.3 seconds 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8168 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 26 sheets defined 52.2% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 54 through 68 removed outlier: 4.302A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 72 through 92 removed outlier: 3.818A pdb=" N GLY A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASN A 92 " --> pdb=" O GLY A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 96 removed outlier: 3.530A pdb=" N ALA A 96 " --> pdb=" O PRO A 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 93 through 96' Processing helix chain 'A' and resid 97 through 126 removed outlier: 3.699A pdb=" N LEU A 105 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 66 removed outlier: 4.376A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 69 No H-bonds generated for 'chain 'B' and resid 67 through 69' Processing helix chain 'B' and resid 70 through 92 removed outlier: 3.586A pdb=" N VAL B 74 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER B 84 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 85 " --> pdb=" O MET B 81 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 126 removed outlier: 3.531A pdb=" N GLY B 101 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 68 removed outlier: 4.050A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 92 removed outlier: 3.580A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY C 79 " --> pdb=" O GLY C 75 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG C 91 " --> pdb=" O ASN C 87 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN C 92 " --> pdb=" O GLY C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 96 Processing helix chain 'C' and resid 99 through 126 removed outlier: 4.465A pdb=" N LEU C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU C 125 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 66 removed outlier: 3.804A pdb=" N SER D 59 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS D 60 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 90 removed outlier: 4.211A pdb=" N GLY D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE D 86 " --> pdb=" O PHE D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 125 removed outlier: 3.577A pdb=" N VAL D 100 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY D 101 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL D 120 " --> pdb=" O PHE D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 removed outlier: 4.372A pdb=" N LYS E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS E 66 " --> pdb=" O VAL E 62 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 90 removed outlier: 3.963A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL E 80 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE E 86 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN E 87 " --> pdb=" O GLY E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 96 removed outlier: 3.631A pdb=" N ALA E 96 " --> pdb=" O PRO E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 111 removed outlier: 3.590A pdb=" N LEU E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 124 removed outlier: 3.575A pdb=" N LEU E 118 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL E 121 " --> pdb=" O SER E 117 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 68 removed outlier: 3.834A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N CYS F 66 " --> pdb=" O VAL F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 92 removed outlier: 4.086A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY F 79 " --> pdb=" O GLY F 75 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE F 86 " --> pdb=" O PHE F 82 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN F 92 " --> pdb=" O GLY F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 120 removed outlier: 3.810A pdb=" N VAL F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY F 101 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU F 105 " --> pdb=" O GLY F 101 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL F 120 " --> pdb=" O PHE F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 127 Processing helix chain 'G' and resid 55 through 68 removed outlier: 3.734A pdb=" N LYS G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS G 66 " --> pdb=" O VAL G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 92 removed outlier: 3.557A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE G 86 " --> pdb=" O PHE G 82 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN G 92 " --> pdb=" O GLY G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 124 removed outlier: 3.642A pdb=" N LEU G 105 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU G 109 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA G 114 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE G 122 " --> pdb=" O LEU G 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 68 removed outlier: 3.500A pdb=" N GLY H 65 " --> pdb=" O MET H 61 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 92 removed outlier: 3.631A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE H 86 " --> pdb=" O PHE H 82 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN H 87 " --> pdb=" O GLY H 83 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN H 92 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 126 removed outlier: 3.909A pdb=" N VAL H 100 " --> pdb=" O ALA H 96 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY H 101 " --> pdb=" O LYS H 97 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU H 109 " --> pdb=" O LEU H 105 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU H 111 " --> pdb=" O PHE H 107 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER H 112 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL H 120 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL H 121 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE H 122 " --> pdb=" O LEU H 118 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU H 125 " --> pdb=" O VAL H 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 66 removed outlier: 4.499A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 92 removed outlier: 4.179A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY I 75 " --> pdb=" O LEU I 71 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN I 92 " --> pdb=" O GLY I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 96 Processing helix chain 'I' and resid 97 through 111 removed outlier: 4.127A pdb=" N LEU I 109 " --> pdb=" O LEU I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 119 Processing helix chain 'I' and resid 119 through 127 removed outlier: 4.026A pdb=" N LEU I 125 " --> pdb=" O VAL I 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 68 removed outlier: 3.899A pdb=" N LYS J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS J 66 " --> pdb=" O VAL J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 90 removed outlier: 4.291A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY J 75 " --> pdb=" O LEU J 71 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL J 80 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 94 No H-bonds generated for 'chain 'J' and resid 92 through 94' Processing helix chain 'J' and resid 95 through 109 removed outlier: 3.808A pdb=" N LEU J 99 " --> pdb=" O ILE J 95 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL J 100 " --> pdb=" O ALA J 96 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU J 105 " --> pdb=" O GLY J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 126 removed outlier: 3.726A pdb=" N ALA J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 64 removed outlier: 3.522A pdb=" N GLU P 64 " --> pdb=" O VAL P 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 84 removed outlier: 3.740A pdb=" N LYS P 82 " --> pdb=" O ILE P 78 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 93 removed outlier: 3.774A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 109 removed outlier: 3.904A pdb=" N ILE P 105 " --> pdb=" O ARG P 101 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER P 107 " --> pdb=" O LYS P 103 " (cutoff:3.500A) Processing helix chain 'P' and resid 117 through 128 Processing helix chain 'P' and resid 130 through 132 No H-bonds generated for 'chain 'P' and resid 130 through 132' Processing helix chain 'P' and resid 133 through 147 removed outlier: 3.626A pdb=" N ASN P 140 " --> pdb=" O GLU P 136 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU P 144 " --> pdb=" O ASN P 140 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 12 removed outlier: 3.618A pdb=" N ALA Q 12 " --> pdb=" O PHE Q 8 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 29 Processing helix chain 'Q' and resid 32 through 37 removed outlier: 3.901A pdb=" N ALA Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 38 removed outlier: 3.587A pdb=" N THR R 34 " --> pdb=" O PRO R 30 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 55 removed outlier: 3.648A pdb=" N TYR R 54 " --> pdb=" O PRO R 51 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR R 55 " --> pdb=" O SER R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 153 through 155 No H-bonds generated for 'chain 'R' and resid 153 through 155' Processing helix chain 'R' and resid 158 through 168 removed outlier: 3.675A pdb=" N SER R 162 " --> pdb=" O ALA R 158 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA R 166 " --> pdb=" O SER R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 197 removed outlier: 3.638A pdb=" N TYR R 188 " --> pdb=" O ALA R 184 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ALA R 197 " --> pdb=" O SER R 193 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 70 removed outlier: 3.728A pdb=" N ILE S 47 " --> pdb=" O VAL S 43 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN S 52 " --> pdb=" O ARG S 48 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS S 58 " --> pdb=" O GLY S 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET S 62 " --> pdb=" O LYS S 58 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS S 69 " --> pdb=" O ALA S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 74 through 79 Processing helix chain 'S' and resid 82 through 89 removed outlier: 3.530A pdb=" N VAL S 86 " --> pdb=" O VAL S 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 114 through 130 removed outlier: 3.545A pdb=" N ILE S 119 " --> pdb=" O LEU S 115 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR S 120 " --> pdb=" O ASN S 116 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG S 124 " --> pdb=" O THR S 120 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR S 129 " --> pdb=" O ALA S 125 " (cutoff:3.500A) Processing helix chain 'S' and resid 146 through 154 removed outlier: 3.869A pdb=" N THR S 151 " --> pdb=" O ARG S 147 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ARG S 152 " --> pdb=" O SER S 148 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE S 153 " --> pdb=" O GLN S 149 " (cutoff:3.500A) Processing helix chain 'S' and resid 171 through 181 Processing helix chain 'S' and resid 238 through 274 removed outlier: 3.617A pdb=" N ARG S 244 " --> pdb=" O SER S 240 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP S 245 " --> pdb=" O ASP S 241 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU S 248 " --> pdb=" O ARG S 244 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA S 268 " --> pdb=" O CYS S 264 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER S 272 " --> pdb=" O ALA S 268 " (cutoff:3.500A) Processing helix chain 'S' and resid 275 through 313 removed outlier: 3.551A pdb=" N LYS S 279 " --> pdb=" O GLU S 275 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 138 removed outlier: 3.884A pdb=" N VAL T 137 " --> pdb=" O ASN T 134 " (cutoff:3.500A) Processing helix chain 'T' and resid 156 through 160 Processing helix chain 'T' and resid 191 through 195 Processing helix chain 'T' and resid 206 through 213 removed outlier: 3.609A pdb=" N LEU T 212 " --> pdb=" O ALA T 208 " (cutoff:3.500A) Processing helix chain 'T' and resid 230 through 247 removed outlier: 3.655A pdb=" N LYS T 243 " --> pdb=" O ILE T 239 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN T 244 " --> pdb=" O ILE T 240 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU T 247 " --> pdb=" O LYS T 243 " (cutoff:3.500A) Processing helix chain 'T' and resid 265 through 280 Processing helix chain 'T' and resid 281 through 283 No H-bonds generated for 'chain 'T' and resid 281 through 283' Processing helix chain 'T' and resid 295 through 301 removed outlier: 3.571A pdb=" N LEU T 301 " --> pdb=" O PRO T 297 " (cutoff:3.500A) Processing helix chain 'T' and resid 301 through 316 removed outlier: 3.557A pdb=" N TYR T 312 " --> pdb=" O ALA T 308 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG T 314 " --> pdb=" O ALA T 310 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 341 removed outlier: 3.569A pdb=" N VAL T 332 " --> pdb=" O SER T 328 " (cutoff:3.500A) Processing helix chain 'T' and resid 346 through 350 Processing helix chain 'T' and resid 351 through 352 No H-bonds generated for 'chain 'T' and resid 351 through 352' Processing helix chain 'T' and resid 353 through 363 removed outlier: 3.928A pdb=" N LEU T 361 " --> pdb=" O LEU T 357 " (cutoff:3.500A) Processing helix chain 'T' and resid 392 through 402 Processing helix chain 'T' and resid 409 through 415 Processing helix chain 'T' and resid 430 through 435 removed outlier: 3.762A pdb=" N ALA T 433 " --> pdb=" O VAL T 430 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA T 434 " --> pdb=" O GLY T 431 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN T 435 " --> pdb=" O SER T 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 430 through 435' Processing helix chain 'T' and resid 436 through 441 removed outlier: 3.803A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) Processing helix chain 'T' and resid 442 through 460 removed outlier: 3.774A pdb=" N LEU T 446 " --> pdb=" O VAL T 442 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU T 455 " --> pdb=" O ALA T 451 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL T 456 " --> pdb=" O GLN T 452 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA T 458 " --> pdb=" O ARG T 454 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE T 459 " --> pdb=" O GLU T 455 " (cutoff:3.500A) Processing helix chain 'T' and resid 469 through 484 removed outlier: 3.611A pdb=" N VAL T 473 " --> pdb=" O ALA T 469 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA T 478 " --> pdb=" O LEU T 474 " (cutoff:3.500A) Processing helix chain 'T' and resid 493 through 506 Processing helix chain 'T' and resid 516 through 527 removed outlier: 5.092A pdb=" N GLU T 522 " --> pdb=" O VAL T 518 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA T 523 " --> pdb=" O ALA T 519 " (cutoff:3.500A) Processing helix chain 'T' and resid 531 through 540 removed outlier: 3.873A pdb=" N ILE T 535 " --> pdb=" O ALA T 531 " (cutoff:3.500A) Processing helix chain 'T' and resid 543 through 552 removed outlier: 3.660A pdb=" N ALA T 548 " --> pdb=" O PRO T 544 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N HIS T 549 " --> pdb=" O ALA T 545 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS T 551 " --> pdb=" O ASP T 547 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 46 Processing helix chain 'U' and resid 47 through 49 No H-bonds generated for 'chain 'U' and resid 47 through 49' Processing helix chain 'U' and resid 58 through 64 removed outlier: 3.532A pdb=" N VAL U 62 " --> pdb=" O LEU U 58 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN U 64 " --> pdb=" O GLN U 60 " (cutoff:3.500A) Processing helix chain 'U' and resid 65 through 73 removed outlier: 3.659A pdb=" N GLU U 72 " --> pdb=" O PRO U 68 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TRP U 73 " --> pdb=" O ALA U 69 " (cutoff:3.500A) Processing helix chain 'U' and resid 134 through 138 removed outlier: 3.706A pdb=" N VAL U 137 " --> pdb=" O ASN U 134 " (cutoff:3.500A) Processing helix chain 'U' and resid 206 through 213 Processing helix chain 'U' and resid 230 through 247 removed outlier: 3.556A pdb=" N ALA U 235 " --> pdb=" O LYS U 231 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN U 242 " --> pdb=" O ALA U 238 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS U 243 " --> pdb=" O ILE U 239 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 265 through 279 Processing helix chain 'U' and resid 280 through 283 removed outlier: 3.517A pdb=" N ARG U 283 " --> pdb=" O GLY U 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 280 through 283' Processing helix chain 'U' and resid 295 through 315 Proline residue: U 303 - end of helix removed outlier: 3.576A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 327 through 341 removed outlier: 3.543A pdb=" N VAL U 332 " --> pdb=" O SER U 328 " (cutoff:3.500A) Processing helix chain 'U' and resid 353 through 363 removed outlier: 3.617A pdb=" N HIS U 358 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU U 361 " --> pdb=" O LEU U 357 " (cutoff:3.500A) Processing helix chain 'U' and resid 369 through 373 Processing helix chain 'U' and resid 392 through 400 Processing helix chain 'U' and resid 409 through 415 Processing helix chain 'U' and resid 436 through 460 removed outlier: 3.547A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU U 446 " --> pdb=" O VAL U 442 " (cutoff:3.500A) Processing helix chain 'U' and resid 470 through 485 removed outlier: 3.507A pdb=" N ALA U 478 " --> pdb=" O LEU U 474 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU U 482 " --> pdb=" O ALA U 478 " (cutoff:3.500A) Processing helix chain 'U' and resid 493 through 506 removed outlier: 3.613A pdb=" N VAL U 499 " --> pdb=" O GLU U 495 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA U 504 " --> pdb=" O ALA U 500 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS U 506 " --> pdb=" O TYR U 502 " (cutoff:3.500A) Processing helix chain 'U' and resid 516 through 528 removed outlier: 3.530A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) Processing helix chain 'U' and resid 530 through 540 removed outlier: 3.774A pdb=" N LYS U 534 " --> pdb=" O PRO U 530 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE U 535 " --> pdb=" O ALA U 531 " (cutoff:3.500A) Processing helix chain 'U' and resid 543 through 554 removed outlier: 3.575A pdb=" N HIS U 549 " --> pdb=" O ALA U 545 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 49 removed outlier: 3.525A pdb=" N ARG V 49 " --> pdb=" O ASP V 46 " (cutoff:3.500A) Processing helix chain 'V' and resid 58 through 67 removed outlier: 3.885A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE V 67 " --> pdb=" O SER V 63 " (cutoff:3.500A) Processing helix chain 'V' and resid 68 through 70 No H-bonds generated for 'chain 'V' and resid 68 through 70' Processing helix chain 'V' and resid 134 through 138 removed outlier: 3.951A pdb=" N VAL V 137 " --> pdb=" O ASN V 134 " (cutoff:3.500A) Processing helix chain 'V' and resid 156 through 160 Processing helix chain 'V' and resid 206 through 213 Processing helix chain 'V' and resid 230 through 247 removed outlier: 3.954A pdb=" N GLU V 247 " --> pdb=" O LYS V 243 " (cutoff:3.500A) Processing helix chain 'V' and resid 265 through 280 Processing helix chain 'V' and resid 281 through 283 No H-bonds generated for 'chain 'V' and resid 281 through 283' Processing helix chain 'V' and resid 295 through 316 Proline residue: V 303 - end of helix removed outlier: 3.592A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG V 314 " --> pdb=" O ALA V 310 " (cutoff:3.500A) Processing helix chain 'V' and resid 326 through 341 Processing helix chain 'V' and resid 353 through 363 removed outlier: 3.603A pdb=" N HIS V 358 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU V 361 " --> pdb=" O LEU V 357 " (cutoff:3.500A) Processing helix chain 'V' and resid 369 through 373 removed outlier: 3.631A pdb=" N GLY V 373 " --> pdb=" O LYS V 370 " (cutoff:3.500A) Processing helix chain 'V' and resid 392 through 402 Processing helix chain 'V' and resid 409 through 414 Processing helix chain 'V' and resid 430 through 435 removed outlier: 4.050A pdb=" N ALA V 433 " --> pdb=" O VAL V 430 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA V 434 " --> pdb=" O GLY V 431 " (cutoff:3.500A) Processing helix chain 'V' and resid 438 through 444 removed outlier: 3.825A pdb=" N VAL V 442 " --> pdb=" O GLY V 438 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) Processing helix chain 'V' and resid 445 through 457 removed outlier: 3.799A pdb=" N GLU V 455 " --> pdb=" O ALA V 451 " (cutoff:3.500A) Processing helix chain 'V' and resid 469 through 482 removed outlier: 3.633A pdb=" N VAL V 473 " --> pdb=" O ALA V 469 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU V 482 " --> pdb=" O ALA V 478 " (cutoff:3.500A) Processing helix chain 'V' and resid 493 through 506 Processing helix chain 'V' and resid 513 through 517 removed outlier: 4.077A pdb=" N ILE V 517 " --> pdb=" O VAL V 514 " (cutoff:3.500A) Processing helix chain 'V' and resid 530 through 540 removed outlier: 3.809A pdb=" N LYS V 534 " --> pdb=" O PRO V 530 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE V 535 " --> pdb=" O ALA V 531 " (cutoff:3.500A) Processing helix chain 'V' and resid 543 through 554 removed outlier: 3.812A pdb=" N HIS V 549 " --> pdb=" O ALA V 545 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS V 551 " --> pdb=" O ASP V 547 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA V 552 " --> pdb=" O ALA V 548 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 118 removed outlier: 3.506A pdb=" N THR X 117 " --> pdb=" O GLY X 114 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU X 118 " --> pdb=" O ARG X 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 114 through 118' Processing helix chain 'X' and resid 149 through 153 removed outlier: 3.564A pdb=" N GLN X 153 " --> pdb=" O PHE X 150 " (cutoff:3.500A) Processing helix chain 'X' and resid 164 through 171 Processing helix chain 'X' and resid 188 through 204 removed outlier: 3.551A pdb=" N ALA X 201 " --> pdb=" O ILE X 197 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS X 202 " --> pdb=" O ASN X 198 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA X 203 " --> pdb=" O ASN X 199 " (cutoff:3.500A) Processing helix chain 'X' and resid 216 through 229 removed outlier: 3.529A pdb=" N GLY X 220 " --> pdb=" O ARG X 216 " (cutoff:3.500A) Processing helix chain 'X' and resid 235 through 242 removed outlier: 3.931A pdb=" N GLU X 238 " --> pdb=" O LEU X 235 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG X 239 " --> pdb=" O GLY X 236 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) Processing helix chain 'X' and resid 254 through 259 Processing helix chain 'X' and resid 260 through 275 removed outlier: 3.562A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 287 through 299 removed outlier: 3.855A pdb=" N THR X 291 " --> pdb=" O ILE X 287 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA X 299 " --> pdb=" O SER X 295 " (cutoff:3.500A) Processing helix chain 'X' and resid 306 through 310 removed outlier: 3.515A pdb=" N TYR X 310 " --> pdb=" O ALA X 307 " (cutoff:3.500A) Processing helix chain 'X' and resid 313 through 323 Processing helix chain 'X' and resid 350 through 355 removed outlier: 3.620A pdb=" N THR X 354 " --> pdb=" O ALA X 350 " (cutoff:3.500A) Processing helix chain 'X' and resid 356 through 358 No H-bonds generated for 'chain 'X' and resid 356 through 358' Processing helix chain 'X' and resid 365 through 371 removed outlier: 3.543A pdb=" N ALA X 369 " --> pdb=" O SER X 365 " (cutoff:3.500A) Processing helix chain 'X' and resid 388 through 393 Processing helix chain 'X' and resid 393 through 412 Processing helix chain 'X' and resid 413 through 420 removed outlier: 3.581A pdb=" N ILE X 419 " --> pdb=" O ASP X 415 " (cutoff:3.500A) Processing helix chain 'X' and resid 421 through 425 removed outlier: 3.875A pdb=" N GLU X 424 " --> pdb=" O GLY X 421 " (cutoff:3.500A) Processing helix chain 'X' and resid 426 through 443 removed outlier: 3.535A pdb=" N THR X 432 " --> pdb=" O GLU X 428 " (cutoff:3.500A) Processing helix chain 'X' and resid 450 through 455 Processing helix chain 'X' and resid 462 through 476 Processing helix chain 'X' and resid 482 through 486 removed outlier: 3.724A pdb=" N ALA X 485 " --> pdb=" O PRO X 482 " (cutoff:3.500A) Processing helix chain 'X' and resid 491 through 505 removed outlier: 3.645A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS X 501 " --> pdb=" O GLU X 497 " (cutoff:3.500A) Processing helix chain 'X' and resid 526 through 533 removed outlier: 3.524A pdb=" N VAL X 531 " --> pdb=" O LEU X 527 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER X 532 " --> pdb=" O ASP X 528 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU X 533 " --> pdb=" O LYS X 529 " (cutoff:3.500A) Processing helix chain 'Y' and resid 114 through 118 Processing helix chain 'Y' and resid 164 through 171 Processing helix chain 'Y' and resid 188 through 201 Processing helix chain 'Y' and resid 216 through 230 Processing helix chain 'Y' and resid 235 through 242 removed outlier: 3.902A pdb=" N GLU Y 238 " --> pdb=" O LEU Y 235 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 254 through 259 Processing helix chain 'Y' and resid 260 through 275 Processing helix chain 'Y' and resid 287 through 299 removed outlier: 3.734A pdb=" N THR Y 291 " --> pdb=" O ILE Y 287 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL Y 297 " --> pdb=" O ALA Y 293 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ALA Y 299 " --> pdb=" O SER Y 295 " (cutoff:3.500A) Processing helix chain 'Y' and resid 313 through 323 Processing helix chain 'Y' and resid 348 through 355 removed outlier: 3.716A pdb=" N THR Y 354 " --> pdb=" O ALA Y 350 " (cutoff:3.500A) Processing helix chain 'Y' and resid 356 through 358 No H-bonds generated for 'chain 'Y' and resid 356 through 358' Processing helix chain 'Y' and resid 365 through 371 removed outlier: 3.533A pdb=" N LEU Y 371 " --> pdb=" O SER Y 367 " (cutoff:3.500A) Processing helix chain 'Y' and resid 388 through 393 Processing helix chain 'Y' and resid 393 through 418 removed outlier: 4.090A pdb=" N VAL Y 399 " --> pdb=" O GLU Y 395 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS Y 411 " --> pdb=" O LEU Y 407 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP Y 415 " --> pdb=" O LYS Y 411 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ILE Y 416 " --> pdb=" O ASN Y 412 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA Y 418 " --> pdb=" O GLN Y 414 " (cutoff:3.500A) Processing helix chain 'Y' and resid 430 through 444 removed outlier: 3.749A pdb=" N SER Y 444 " --> pdb=" O GLN Y 440 " (cutoff:3.500A) Processing helix chain 'Y' and resid 462 through 475 removed outlier: 3.522A pdb=" N GLY Y 472 " --> pdb=" O SER Y 468 " (cutoff:3.500A) Processing helix chain 'Y' and resid 495 through 508 removed outlier: 3.772A pdb=" N ASP Y 500 " --> pdb=" O LYS Y 496 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS Y 501 " --> pdb=" O GLU Y 497 " (cutoff:3.500A) Processing helix chain 'Y' and resid 509 through 512 removed outlier: 3.941A pdb=" N ALA Y 512 " --> pdb=" O ARG Y 509 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 509 through 512' Processing helix chain 'Y' and resid 526 through 533 Processing helix chain 'Y' and resid 544 through 555 removed outlier: 3.580A pdb=" N LYS Y 550 " --> pdb=" O GLU Y 546 " (cutoff:3.500A) Processing helix chain 'Z' and resid 114 through 118 Processing helix chain 'Z' and resid 164 through 170 Processing helix chain 'Z' and resid 188 through 203 Processing helix chain 'Z' and resid 216 through 230 Processing helix chain 'Z' and resid 235 through 242 removed outlier: 4.144A pdb=" N GLU Z 238 " --> pdb=" O LEU Z 235 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 254 through 260 Processing helix chain 'Z' and resid 260 through 275 removed outlier: 3.510A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 286 through 301 Processing helix chain 'Z' and resid 306 through 310 removed outlier: 3.614A pdb=" N TYR Z 310 " --> pdb=" O ALA Z 307 " (cutoff:3.500A) Processing helix chain 'Z' and resid 313 through 323 removed outlier: 3.860A pdb=" N LEU Z 321 " --> pdb=" O ASP Z 317 " (cutoff:3.500A) Processing helix chain 'Z' and resid 348 through 355 Processing helix chain 'Z' and resid 365 through 370 Processing helix chain 'Z' and resid 392 through 412 removed outlier: 4.279A pdb=" N HIS Z 396 " --> pdb=" O ILE Z 392 " (cutoff:3.500A) Processing helix chain 'Z' and resid 413 through 418 removed outlier: 4.084A pdb=" N ALA Z 418 " --> pdb=" O GLN Z 414 " (cutoff:3.500A) Processing helix chain 'Z' and resid 428 through 441 removed outlier: 3.525A pdb=" N LYS Z 438 " --> pdb=" O ALA Z 434 " (cutoff:3.500A) Processing helix chain 'Z' and resid 447 through 449 No H-bonds generated for 'chain 'Z' and resid 447 through 449' Processing helix chain 'Z' and resid 450 through 455 removed outlier: 3.693A pdb=" N GLY Z 455 " --> pdb=" O GLU Z 451 " (cutoff:3.500A) Processing helix chain 'Z' and resid 462 through 476 removed outlier: 3.622A pdb=" N GLY Z 472 " --> pdb=" O SER Z 468 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL Z 473 " --> pdb=" O GLY Z 469 " (cutoff:3.500A) Processing helix chain 'Z' and resid 494 through 505 Processing helix chain 'Z' and resid 506 through 507 No H-bonds generated for 'chain 'Z' and resid 506 through 507' Processing helix chain 'Z' and resid 508 through 512 removed outlier: 3.895A pdb=" N GLU Z 511 " --> pdb=" O SER Z 508 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA Z 512 " --> pdb=" O ARG Z 509 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 508 through 512' Processing helix chain 'Z' and resid 526 through 532 Processing sheet with id=AA1, first strand: chain 'Q' and resid 61 through 65 removed outlier: 9.842A pdb=" N VAL S 137 " --> pdb=" O TYR S 158 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N LEU S 160 " --> pdb=" O VAL S 137 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL S 139 " --> pdb=" O LEU S 160 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N ILE S 162 " --> pdb=" O VAL S 139 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N SER S 141 " --> pdb=" O ILE S 162 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N SER S 100 " --> pdb=" O VAL S 138 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N VAL S 140 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL S 102 " --> pdb=" O VAL S 140 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE S 142 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA S 104 " --> pdb=" O ILE S 142 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LYS S 99 " --> pdb=" O SER S 189 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N GLN S 191 " --> pdb=" O LYS S 99 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL S 101 " --> pdb=" O GLN S 191 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU S 193 " --> pdb=" O VAL S 101 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL S 103 " --> pdb=" O LEU S 193 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N ASN S 195 " --> pdb=" O VAL S 103 " (cutoff:3.500A) removed outlier: 9.400A pdb=" N VAL S 105 " --> pdb=" O ASN S 195 " (cutoff:3.500A) removed outlier: 10.723A pdb=" N PHE S 197 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS S 204 " --> pdb=" O LYS S 196 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 80 through 82 Processing sheet with id=AA3, first strand: chain 'R' and resid 80 through 82 removed outlier: 7.434A pdb=" N ILE R 108 " --> pdb=" O GLU S 234 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'R' and resid 97 through 100 removed outlier: 6.637A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'T' and resid 116 through 122 removed outlier: 3.766A pdb=" N GLU T 107 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU T 108 " --> pdb=" O THR T 147 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ARG T 96 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL T 90 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE T 94 " --> pdb=" O VAL T 90 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN T 121 " --> pdb=" O GLY T 128 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N PHE T 132 " --> pdb=" O GLY T 117 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLY T 117 " --> pdb=" O PHE T 132 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEU Y 72 " --> pdb=" O VAL Y 65 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N VAL Y 76 " --> pdb=" O ILE Y 88 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE Y 88 " --> pdb=" O VAL Y 76 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL Y 47 " --> pdb=" O VAL Y 43 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL Y 43 " --> pdb=" O VAL Y 47 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASP Y 49 " --> pdb=" O SER Y 41 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'T' and resid 152 through 155 Processing sheet with id=AA7, first strand: chain 'T' and resid 163 through 164 removed outlier: 6.319A pdb=" N THR T 164 " --> pdb=" O SER T 289 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU T 222 " --> pdb=" O ILE T 406 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'T' and resid 201 through 202 removed outlier: 4.491A pdb=" N ILE T 215 " --> pdb=" O LEU T 202 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'U' and resid 116 through 122 removed outlier: 4.045A pdb=" N GLU U 107 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N LEU U 108 " --> pdb=" O THR U 147 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N VAL U 87 " --> pdb=" O TYR U 98 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N TYR U 98 " --> pdb=" O VAL U 87 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N PHE U 132 " --> pdb=" O GLY U 117 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N GLY U 117 " --> pdb=" O PHE U 132 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N VAL X 76 " --> pdb=" O ILE X 88 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE X 88 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL X 47 " --> pdb=" O VAL X 43 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL X 43 " --> pdb=" O VAL X 47 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASP X 49 " --> pdb=" O SER X 41 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'U' and resid 152 through 155 Processing sheet with id=AB2, first strand: chain 'U' and resid 163 through 164 removed outlier: 6.650A pdb=" N LEU U 222 " --> pdb=" O ILE U 406 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LEU U 408 " --> pdb=" O LEU U 222 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE U 224 " --> pdb=" O LEU U 408 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'V' and resid 116 through 122 removed outlier: 3.841A pdb=" N GLU V 107 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU V 108 " --> pdb=" O THR V 147 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ARG V 96 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N HIS V 126 " --> pdb=" O LEU V 122 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N LEU V 122 " --> pdb=" O HIS V 126 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLY V 128 " --> pdb=" O LEU V 120 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG Z 86 " --> pdb=" O ALA Z 77 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N HIS Z 79 " --> pdb=" O THR Z 84 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N THR Z 84 " --> pdb=" O HIS Z 79 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'V' and resid 152 through 155 Processing sheet with id=AB5, first strand: chain 'V' and resid 163 through 164 removed outlier: 6.357A pdb=" N THR V 164 " --> pdb=" O SER V 289 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU V 222 " --> pdb=" O ILE V 406 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU V 408 " --> pdb=" O LEU V 222 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE V 224 " --> pdb=" O LEU V 408 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'V' and resid 201 through 202 removed outlier: 4.493A pdb=" N ILE V 215 " --> pdb=" O LEU V 202 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'X' and resid 110 through 113 Processing sheet with id=AB8, first strand: chain 'X' and resid 121 through 122 removed outlier: 6.220A pdb=" N MET X 122 " --> pdb=" O TYR X 248 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER X 208 " --> pdb=" O THR X 245 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N VAL X 247 " --> pdb=" O SER X 208 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N PHE X 210 " --> pdb=" O VAL X 247 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N GLY X 249 " --> pdb=" O PHE X 210 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLY X 212 " --> pdb=" O GLY X 249 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE X 179 " --> pdb=" O GLN X 337 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL X 339 " --> pdb=" O ILE X 179 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LEU X 181 " --> pdb=" O VAL X 339 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LYS X 178 " --> pdb=" O ALA X 360 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N THR X 362 " --> pdb=" O LYS X 178 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLY X 180 " --> pdb=" O THR X 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'X' and resid 159 through 160 removed outlier: 4.269A pdb=" N TYR X 173 " --> pdb=" O LEU X 160 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'X' and resid 559 through 561 Processing sheet with id=AC2, first strand: chain 'Y' and resid 110 through 111 Processing sheet with id=AC3, first strand: chain 'Y' and resid 121 through 122 removed outlier: 6.230A pdb=" N MET Y 122 " --> pdb=" O TYR Y 248 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL Y 213 " --> pdb=" O ASP Y 285 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE Y 179 " --> pdb=" O GLN Y 337 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL Y 339 " --> pdb=" O ILE Y 179 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LEU Y 181 " --> pdb=" O VAL Y 339 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Y' and resid 159 through 160 removed outlier: 4.305A pdb=" N TYR Y 173 " --> pdb=" O LEU Y 160 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Z' and resid 110 through 113 Processing sheet with id=AC6, first strand: chain 'Z' and resid 121 through 122 removed outlier: 6.038A pdb=" N MET Z 122 " --> pdb=" O TYR Z 248 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N GLN Z 250 " --> pdb=" O MET Z 122 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL Z 213 " --> pdb=" O ASP Z 285 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL Z 280 " --> pdb=" O THR Z 334 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N VAL Z 336 " --> pdb=" O VAL Z 280 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU Z 282 " --> pdb=" O VAL Z 336 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ALA Z 338 " --> pdb=" O LEU Z 282 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL Z 284 " --> pdb=" O ALA Z 338 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ILE Z 179 " --> pdb=" O GLN Z 337 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LYS Z 178 " --> pdb=" O ALA Z 360 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N THR Z 362 " --> pdb=" O LYS Z 178 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLY Z 180 " --> pdb=" O THR Z 362 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Z' and resid 159 through 160 removed outlier: 4.318A pdb=" N TYR Z 173 " --> pdb=" O LEU Z 160 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Z' and resid 559 through 561 1598 hydrogen bonds defined for protein. 4593 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.28 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8590 1.33 - 1.45: 5891 1.45 - 1.57: 19739 1.57 - 1.69: 23 1.69 - 1.81: 200 Bond restraints: 34443 Sorted by residual: bond pdb=" N PRO X 349 " pdb=" CA PRO X 349 " ideal model delta sigma weight residual 1.469 1.689 -0.220 1.28e-02 6.10e+03 2.95e+02 bond pdb=" C4 ADP Y 601 " pdb=" C5 ADP Y 601 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C4 ADP X 601 " pdb=" C5 ADP X 601 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C ASP X 348 " pdb=" N PRO X 349 " ideal model delta sigma weight residual 1.334 1.448 -0.114 2.34e-02 1.83e+03 2.38e+01 bond pdb=" C5 ADP Y 601 " pdb=" C6 ADP Y 601 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.69e+01 ... (remaining 34438 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.79: 46288 3.79 - 7.58: 339 7.58 - 11.38: 45 11.38 - 15.17: 5 15.17 - 18.96: 2 Bond angle restraints: 46679 Sorted by residual: angle pdb=" C ASP X 348 " pdb=" N PRO X 349 " pdb=" CA PRO X 349 " ideal model delta sigma weight residual 119.84 138.80 -18.96 1.25e+00 6.40e-01 2.30e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 130.61 9.26 1.00e+00 1.00e+00 8.58e+01 angle pdb=" CA PRO X 349 " pdb=" N PRO X 349 " pdb=" CD PRO X 349 " ideal model delta sigma weight residual 112.00 99.71 12.29 1.40e+00 5.10e-01 7.70e+01 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 131.53 8.34 1.00e+00 1.00e+00 6.96e+01 angle pdb=" N GLU J 111 " pdb=" CA GLU J 111 " pdb=" C GLU J 111 " ideal model delta sigma weight residual 112.23 102.58 9.65 1.26e+00 6.30e-01 5.87e+01 ... (remaining 46674 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.60: 19591 24.60 - 49.19: 997 49.19 - 73.79: 130 73.79 - 98.38: 26 98.38 - 122.98: 2 Dihedral angle restraints: 20746 sinusoidal: 7978 harmonic: 12768 Sorted by residual: dihedral pdb=" O1B ADP X 601 " pdb=" O3A ADP X 601 " pdb=" PB ADP X 601 " pdb=" PA ADP X 601 " ideal model delta sinusoidal sigma weight residual 300.00 177.02 122.98 1 2.00e+01 2.50e-03 3.71e+01 dihedral pdb=" C5' ADP Y 601 " pdb=" O5' ADP Y 601 " pdb=" PA ADP Y 601 " pdb=" O2A ADP Y 601 " ideal model delta sinusoidal sigma weight residual -60.00 59.62 -119.62 1 2.00e+01 2.50e-03 3.59e+01 dihedral pdb=" CA ASP T 326 " pdb=" C ASP T 326 " pdb=" N LEU T 327 " pdb=" CA LEU T 327 " ideal model delta harmonic sigma weight residual 180.00 151.07 28.93 0 5.00e+00 4.00e-02 3.35e+01 ... (remaining 20743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 4534 0.078 - 0.155: 865 0.155 - 0.233: 109 0.233 - 0.310: 16 0.310 - 0.388: 2 Chirality restraints: 5526 Sorted by residual: chirality pdb=" CA ASP S 83 " pdb=" N ASP S 83 " pdb=" C ASP S 83 " pdb=" CB ASP S 83 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" CB VAL U 180 " pdb=" CA VAL U 180 " pdb=" CG1 VAL U 180 " pdb=" CG2 VAL U 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CA PRO X 349 " pdb=" N PRO X 349 " pdb=" C PRO X 349 " pdb=" CB PRO X 349 " both_signs ideal model delta sigma weight residual False 2.72 3.02 -0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 5523 not shown) Planarity restraints: 5999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS T 415 " -0.015 2.00e-02 2.50e+03 2.99e-02 8.93e+00 pdb=" C LYS T 415 " 0.052 2.00e-02 2.50e+03 pdb=" O LYS T 415 " -0.020 2.00e-02 2.50e+03 pdb=" N GLY T 416 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU Q 33 " -0.049 5.00e-02 4.00e+02 7.43e-02 8.82e+00 pdb=" N PRO Q 34 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO Q 34 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO Q 34 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP Z 348 " -0.047 5.00e-02 4.00e+02 7.19e-02 8.26e+00 pdb=" N PRO Z 349 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO Z 349 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO Z 349 " -0.040 5.00e-02 4.00e+02 ... (remaining 5996 not shown) Histogram of nonbonded interaction distances: 0.35 - 1.26: 3 1.26 - 2.17: 20 2.17 - 3.08: 21032 3.08 - 3.99: 93700 3.99 - 4.90: 179798 Warning: very small nonbonded interaction distances. Nonbonded interactions: 294553 Sorted by model distance: nonbonded pdb="MG MG X 602 " pdb=" O HOH X 703 " model vdw 0.351 2.170 nonbonded pdb=" OH TYR V 259 " pdb=" OD2 ASP V 325 " model vdw 0.928 3.040 nonbonded pdb=" CZ TYR V 259 " pdb=" OD2 ASP V 325 " model vdw 1.165 3.260 nonbonded pdb=" OH TYR V 259 " pdb=" CG ASP V 325 " model vdw 1.597 3.270 nonbonded pdb=" OE1 GLU X 215 " pdb=" O HOH X 701 " model vdw 1.599 3.040 ... (remaining 294548 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'T' selection = (chain 'U' and (resid 80 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) selection = (chain 'V' and resid 80 through 1002) } ncs_group { reference = (chain 'X' and resid 37 through 556) selection = (chain 'Y' and resid 37 through 556) selection = (chain 'Z' and resid 37 through 556) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.050 Extract box with map and model: 0.640 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 30.180 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.220 34443 Z= 0.407 Angle : 0.997 18.960 46679 Z= 0.583 Chirality : 0.062 0.388 5526 Planarity : 0.007 0.074 5999 Dihedral : 14.820 122.975 12578 Min Nonbonded Distance : 0.351 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.08 % Favored : 95.79 % Rotamer: Outliers : 1.23 % Allowed : 7.88 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.44 (0.10), residues: 4463 helix: -4.11 (0.06), residues: 2130 sheet: -1.12 (0.21), residues: 571 loop : -1.69 (0.13), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG U 217 TYR 0.017 0.002 TYR U 57 PHE 0.027 0.002 PHE S 249 TRP 0.017 0.002 TRP X 141 HIS 0.009 0.002 HIS S 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00828 / 0.41 (34443) covalent geometry : angle 0.99709 / 0.58 (46679) hydrogen bonds : bond 0.28097 / 18.50 ( 1596) hydrogen bonds : angle 10.43797 / 7.23 ( 4593) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 3569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 600 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 97 LYS cc_start: 0.8632 (mppt) cc_final: 0.8423 (mttp) REVERT: E 56 LEU cc_start: 0.7670 (pt) cc_final: 0.6850 (mt) REVERT: E 60 LYS cc_start: 0.7275 (mtmt) cc_final: 0.7011 (ptpp) REVERT: E 100 VAL cc_start: 0.7164 (t) cc_final: 0.6850 (m) REVERT: G 61 MET cc_start: 0.7353 (mtm) cc_final: 0.7036 (mmt) REVERT: I 81 MET cc_start: 0.7282 (ttp) cc_final: 0.6745 (ppp) REVERT: I 119 LEU cc_start: 0.6734 (mp) cc_final: 0.6371 (pp) REVERT: J 66 CYS cc_start: 0.7471 (m) cc_final: 0.7014 (m) REVERT: P 63 LYS cc_start: 0.8457 (tppt) cc_final: 0.8164 (tppp) REVERT: P 69 LYS cc_start: 0.7885 (tttm) cc_final: 0.7652 (tptp) REVERT: P 72 ASP cc_start: 0.8056 (t0) cc_final: 0.7654 (t0) REVERT: P 73 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7771 (mt-10) REVERT: P 119 LYS cc_start: 0.8798 (mtpt) cc_final: 0.8348 (mmmm) REVERT: P 140 ASN cc_start: 0.8995 (m-40) cc_final: 0.8788 (m110) REVERT: P 145 MET cc_start: 0.8481 (mmm) cc_final: 0.8144 (mmm) REVERT: Q 10 ARG cc_start: 0.7827 (tpp-160) cc_final: 0.7391 (ttt90) REVERT: S 62 MET cc_start: 0.7486 (ptp) cc_final: 0.7226 (ptt) REVERT: S 219 GLN cc_start: 0.6956 (mt0) cc_final: 0.6698 (tp-100) REVERT: T 475 GLU cc_start: 0.7255 (tp30) cc_final: 0.6822 (tp30) REVERT: U 71 LYS cc_start: 0.8422 (tppt) cc_final: 0.8178 (tppp) REVERT: V 61 HIS cc_start: 0.7750 (t70) cc_final: 0.7378 (m170) REVERT: X 189 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8194 (mtmm) REVERT: X 385 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7282 (tpt90) REVERT: X 415 ASP cc_start: 0.7598 (t70) cc_final: 0.7363 (t0) REVERT: X 484 MET cc_start: 0.8069 (mmt) cc_final: 0.7622 (tpp) REVERT: X 573 LYS cc_start: 0.7823 (mtmt) cc_final: 0.7491 (mmtm) REVERT: Y 243 LYS cc_start: 0.8299 (mtpt) cc_final: 0.7957 (mmtm) REVERT: Y 313 THR cc_start: 0.9236 (p) cc_final: 0.9010 (p) REVERT: Y 385 ARG cc_start: 0.8042 (mmt90) cc_final: 0.7789 (mmm-85) REVERT: Y 437 ARG cc_start: 0.7709 (mtt-85) cc_final: 0.7466 (mmm-85) REVERT: Y 484 MET cc_start: 0.8116 (tpp) cc_final: 0.7877 (tpt) REVERT: Y 501 LYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6646 (tmmm) REVERT: Z 493 LYS cc_start: 0.7809 (mtmt) cc_final: 0.7600 (mttt) outliers start: 44 outliers final: 20 residues processed: 641 average time/residue: 0.7024 time to fit residues: 536.4489 Evaluate side-chains 452 residues out of total 3569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 429 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 103 VAL Chi-restraints excluded: chain T residue 267 SER Chi-restraints excluded: chain T residue 268 THR Chi-restraints excluded: chain T residue 339 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 345 PRO Chi-restraints excluded: chain U residue 348 GLU Chi-restraints excluded: chain V residue 267 SER Chi-restraints excluded: chain V residue 268 THR Chi-restraints excluded: chain V residue 323 ILE Chi-restraints excluded: chain V residue 325 ASP Chi-restraints excluded: chain V residue 329 LYS Chi-restraints excluded: chain V residue 417 ILE Chi-restraints excluded: chain V residue 487 LYS Chi-restraints excluded: chain X residue 189 LYS Chi-restraints excluded: chain X residue 287 ILE Chi-restraints excluded: chain X residue 385 ARG Chi-restraints excluded: chain Y residue 306 SER Chi-restraints excluded: chain Y residue 501 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: [432, 197, 388, 215, 20, 132, 261, 248, 207, 401, 424] chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.6980 chunk 401 optimal weight: 1.9990 chunk 424 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN H 98 GLN J 92 ASN J 98 GLN P 83 GLN ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 73 ASN R 85 GLN R 104 HIS R 137 HIS S 186 ASN S 293 ASN S 297 GLN T 264 GLN T 386 GLN T 441 GLN T 488 GLN T 497 GLN T 529 ASN U 121 ASN U 196 GLN U 242 GLN U 246 ASN U 248 GLN U 319 HIS U 386 GLN U 441 GLN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 527 GLN V 104 GLN ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 126 HIS V 139 HIS ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 244 ASN V 271 GLN V 486 GLN V 497 GLN X 199 ASN X 241 ASN X 278 GLN X 286 ASN X 337 GLN X 471 GLN Y 241 ASN Z 199 ASN Z 278 GLN ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 408 GLN Z 448 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.144676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.102279 restraints weight = 44854.860| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.82 r_work: 0.3031 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 34443 Z= 0.155 Angle : 0.628 8.782 46679 Z= 0.325 Chirality : 0.045 0.293 5526 Planarity : 0.005 0.058 5999 Dihedral : 6.943 121.399 4876 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.20 % Favored : 96.73 % Rotamer: Outliers : 2.63 % Allowed : 15.08 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.11), residues: 4463 helix: -2.14 (0.09), residues: 2217 sheet: -0.92 (0.21), residues: 562 loop : -1.16 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 124 TYR 0.014 0.001 TYR Z 310 PHE 0.021 0.001 PHE B 107 TRP 0.010 0.001 TRP R 37 HIS 0.005 0.001 HIS V 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (34443) covalent geometry : angle 0.62816 / 0.32 (46679) hydrogen bonds : bond 0.04495 / 2.95 ( 1596) hydrogen bonds : angle 5.40494 / 3.72 ( 4593) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 484 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.7655 (mpp) cc_final: 0.7354 (mtm) REVERT: B 107 PHE cc_start: 0.7113 (t80) cc_final: 0.6753 (t80) REVERT: C 97 LYS cc_start: 0.8707 (mppt) cc_final: 0.8451 (mttm) REVERT: D 61 MET cc_start: 0.7898 (mpt) cc_final: 0.7606 (mmt) REVERT: E 92 ASN cc_start: 0.7695 (p0) cc_final: 0.7310 (p0) REVERT: F 81 MET cc_start: 0.8125 (ttp) cc_final: 0.7836 (ttp) REVERT: F 111 GLU cc_start: 0.8179 (tp30) cc_final: 0.7889 (mm-30) REVERT: F 120 VAL cc_start: 0.8233 (t) cc_final: 0.7985 (p) REVERT: G 87 ASN cc_start: 0.7069 (m110) cc_final: 0.6787 (m110) REVERT: G 95 ILE cc_start: 0.7954 (mm) cc_final: 0.7602 (mm) REVERT: H 61 MET cc_start: 0.6868 (tpp) cc_final: 0.6611 (mmp) REVERT: H 105 LEU cc_start: 0.8166 (tm) cc_final: 0.7965 (tt) REVERT: H 116 PHE cc_start: 0.7433 (m-10) cc_final: 0.7218 (m-80) REVERT: I 119 LEU cc_start: 0.6627 (OUTLIER) cc_final: 0.6202 (pp) REVERT: J 59 SER cc_start: 0.7158 (p) cc_final: 0.6826 (p) REVERT: J 66 CYS cc_start: 0.8098 (m) cc_final: 0.7606 (m) REVERT: P 49 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.8132 (t) REVERT: P 63 LYS cc_start: 0.8677 (tppt) cc_final: 0.8366 (tppp) REVERT: P 69 LYS cc_start: 0.7765 (tttm) cc_final: 0.7539 (tptm) REVERT: P 71 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7502 (tt0) REVERT: P 72 ASP cc_start: 0.8228 (t0) cc_final: 0.7805 (t0) REVERT: P 122 PHE cc_start: 0.8328 (m-80) cc_final: 0.8027 (m-80) REVERT: P 136 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8324 (tp30) REVERT: P 145 MET cc_start: 0.8666 (mmm) cc_final: 0.8398 (mmm) REVERT: Q 10 ARG cc_start: 0.7749 (tpp-160) cc_final: 0.7208 (ttt90) REVERT: Q 40 GLN cc_start: 0.7537 (mm-40) cc_final: 0.7082 (tm130) REVERT: R 49 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7465 (mm-30) REVERT: R 107 THR cc_start: 0.8052 (m) cc_final: 0.7802 (p) REVERT: S 62 MET cc_start: 0.8317 (ptp) cc_final: 0.7842 (ptt) REVERT: S 169 ARG cc_start: 0.7895 (ptm160) cc_final: 0.7289 (ptm160) REVERT: S 186 ASN cc_start: 0.7926 (OUTLIER) cc_final: 0.7726 (t0) REVERT: S 190 TYR cc_start: 0.8483 (m-80) cc_final: 0.8151 (m-80) REVERT: T 237 ASP cc_start: 0.8539 (m-30) cc_final: 0.8317 (m-30) REVERT: T 475 GLU cc_start: 0.7110 (tp30) cc_final: 0.6651 (tp30) REVERT: T 479 ARG cc_start: 0.7827 (mpt90) cc_final: 0.7509 (mpt180) REVERT: U 45 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7484 (mp) REVERT: U 71 LYS cc_start: 0.8371 (tppt) cc_final: 0.8086 (tppp) REVERT: U 84 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8979 (mp) REVERT: U 127 VAL cc_start: 0.8874 (OUTLIER) cc_final: 0.8620 (m) REVERT: U 482 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7733 (mm-30) REVERT: U 511 LYS cc_start: 0.7887 (mttt) cc_final: 0.7473 (mmtm) REVERT: U 515 GLN cc_start: 0.7715 (mp10) cc_final: 0.7156 (pt0) REVERT: V 471 GLN cc_start: 0.6678 (pp30) cc_final: 0.6259 (tm130) REVERT: X 158 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7630 (pm20) REVERT: X 279 ASP cc_start: 0.8450 (m-30) cc_final: 0.8208 (m-30) REVERT: X 415 ASP cc_start: 0.8071 (t70) cc_final: 0.7852 (t0) REVERT: X 484 MET cc_start: 0.8644 (mmt) cc_final: 0.8238 (tpp) REVERT: X 572 LYS cc_start: 0.7700 (tptp) cc_final: 0.7434 (tmmt) REVERT: X 573 LYS cc_start: 0.7622 (mtmt) cc_final: 0.7112 (mmtm) REVERT: Y 51 ARG cc_start: 0.8800 (ttt-90) cc_final: 0.8438 (ttt-90) REVERT: Y 385 ARG cc_start: 0.8442 (mmt90) cc_final: 0.8150 (mmm-85) REVERT: Y 437 ARG cc_start: 0.7471 (mtt-85) cc_final: 0.7096 (mmm-85) REVERT: Y 484 MET cc_start: 0.8220 (tpp) cc_final: 0.7915 (tpt) REVERT: Z 152 GLU cc_start: 0.8530 (tp30) cc_final: 0.8323 (mm-30) REVERT: Z 292 GLN cc_start: 0.8433 (tt0) cc_final: 0.7977 (tt0) REVERT: Z 437 ARG cc_start: 0.8053 (mtp85) cc_final: 0.7769 (mtm110) REVERT: Z 484 MET cc_start: 0.7105 (mmm) cc_final: 0.6481 (tmt) REVERT: Z 493 LYS cc_start: 0.7819 (mtmt) cc_final: 0.7545 (mttt) REVERT: Z 573 LYS cc_start: 0.7366 (tppt) cc_final: 0.7075 (ttmt) outliers start: 94 outliers final: 32 residues processed: 542 average time/residue: 0.6587 time to fit residues: 428.8039 Evaluate side-chains 455 residues out of total 3569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 414 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 71 GLN Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain P residue 136 GLU Chi-restraints excluded: chain R residue 182 ARG Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 86 VAL Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 186 ASN Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 182 SER Chi-restraints excluded: chain T residue 183 SER Chi-restraints excluded: chain T residue 267 SER Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 348 GLU Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 323 ILE Chi-restraints excluded: chain V residue 326 ASP Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain X residue 158 GLU Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 480 ASP Chi-restraints excluded: chain Z residue 55 GLU Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 492 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: [310, 112, 59, 183, 108, 191, 88, 328, 103, 261, 312] chunk 310 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 191 optimal weight: 0.0270 chunk 88 optimal weight: 0.8980 chunk 328 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 261 optimal weight: 0.7980 chunk 312 optimal weight: 0.6980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 98 GLN J 92 ASN P 83 GLN ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 ASN T 104 GLN T 358 HIS T 435 GLN T 529 ASN U 549 HIS ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 241 HIS V 264 GLN V 515 GLN V 549 HIS ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.145561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.101904 restraints weight = 44830.649| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.61 r_work: 0.3068 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34443 Z= 0.124 Angle : 0.560 9.371 46679 Z= 0.287 Chirality : 0.043 0.155 5526 Planarity : 0.004 0.045 5999 Dihedral : 5.974 108.597 4835 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.38 % Favored : 96.57 % Rotamer: Outliers : 3.00 % Allowed : 16.82 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.12), residues: 4463 helix: -0.96 (0.11), residues: 2187 sheet: -0.78 (0.21), residues: 563 loop : -0.90 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 496 TYR 0.016 0.001 TYR V 414 PHE 0.021 0.001 PHE H 107 TRP 0.007 0.001 TRP R 37 HIS 0.003 0.001 HIS S 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (34443) covalent geometry : angle 0.56006 / 0.29 (46679) hydrogen bonds : bond 0.03861 / 2.55 ( 1596) hydrogen bonds : angle 4.84233 / 3.34 ( 4593) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 3569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 458 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.7688 (mpp) cc_final: 0.7463 (mtm) REVERT: B 81 MET cc_start: 0.8413 (tpp) cc_final: 0.8159 (tpp) REVERT: C 69 ILE cc_start: 0.8191 (pt) cc_final: 0.7971 (pp) REVERT: C 97 LYS cc_start: 0.8696 (mppt) cc_final: 0.8376 (mttm) REVERT: D 61 MET cc_start: 0.8041 (mpt) cc_final: 0.7729 (mmt) REVERT: E 60 LYS cc_start: 0.6561 (ptpp) cc_final: 0.6348 (mtmp) REVERT: E 95 ILE cc_start: 0.8121 (mm) cc_final: 0.7672 (mp) REVERT: F 81 MET cc_start: 0.8174 (ttp) cc_final: 0.7794 (ttp) REVERT: F 111 GLU cc_start: 0.8170 (tp30) cc_final: 0.7905 (mm-30) REVERT: G 87 ASN cc_start: 0.7086 (m110) cc_final: 0.6856 (m110) REVERT: G 95 ILE cc_start: 0.8017 (mm) cc_final: 0.7694 (mm) REVERT: H 116 PHE cc_start: 0.7455 (m-10) cc_final: 0.7243 (m-80) REVERT: I 119 LEU cc_start: 0.6689 (mp) cc_final: 0.6214 (pp) REVERT: J 59 SER cc_start: 0.7367 (p) cc_final: 0.6966 (p) REVERT: J 61 MET cc_start: 0.7416 (mpt) cc_final: 0.7146 (mpt) REVERT: J 66 CYS cc_start: 0.8049 (m) cc_final: 0.7642 (m) REVERT: J 71 LEU cc_start: 0.8095 (mp) cc_final: 0.7851 (tp) REVERT: J 92 ASN cc_start: 0.8074 (OUTLIER) cc_final: 0.7869 (p0) REVERT: P 49 THR cc_start: 0.8376 (OUTLIER) cc_final: 0.8086 (t) REVERT: P 63 LYS cc_start: 0.8681 (tppt) cc_final: 0.8475 (tptm) REVERT: P 68 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7284 (t0) REVERT: P 71 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7553 (tt0) REVERT: P 72 ASP cc_start: 0.8014 (t0) cc_final: 0.7749 (t0) REVERT: P 73 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8124 (mt-10) REVERT: P 122 PHE cc_start: 0.8352 (m-80) cc_final: 0.8043 (m-80) REVERT: P 136 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8352 (tp30) REVERT: P 145 MET cc_start: 0.8691 (mmm) cc_final: 0.8407 (mmm) REVERT: Q 10 ARG cc_start: 0.7779 (tpp-160) cc_final: 0.7242 (ttm-80) REVERT: Q 40 GLN cc_start: 0.7354 (mm-40) cc_final: 0.7060 (tm-30) REVERT: R 127 PHE cc_start: 0.7463 (m-80) cc_final: 0.7245 (m-80) REVERT: R 182 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.6903 (ttt180) REVERT: S 169 ARG cc_start: 0.7951 (ptm160) cc_final: 0.7662 (ptm160) REVERT: S 190 TYR cc_start: 0.8422 (m-80) cc_final: 0.8064 (m-80) REVERT: S 234 GLU cc_start: 0.8159 (tm-30) cc_final: 0.6874 (tm-30) REVERT: S 275 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7494 (tm-30) REVERT: U 71 LYS cc_start: 0.8354 (tppt) cc_final: 0.8107 (tppp) REVERT: U 84 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8963 (mp) REVERT: U 127 VAL cc_start: 0.8814 (OUTLIER) cc_final: 0.8596 (m) REVERT: U 482 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7814 (mm-30) REVERT: U 511 LYS cc_start: 0.7795 (mttt) cc_final: 0.7200 (mttm) REVERT: V 67 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8299 (mt) REVERT: V 149 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7849 (mm-40) REVERT: V 449 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7586 (mt-10) REVERT: V 455 GLU cc_start: 0.7830 (pt0) cc_final: 0.7369 (pp20) REVERT: X 215 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7802 (mm-30) REVERT: X 471 GLN cc_start: 0.8112 (tt0) cc_final: 0.7704 (tp-100) REVERT: X 573 LYS cc_start: 0.7736 (mtmt) cc_final: 0.7394 (mtpt) REVERT: Y 51 ARG cc_start: 0.8753 (ttt-90) cc_final: 0.8373 (ttt-90) REVERT: Y 385 ARG cc_start: 0.8364 (mmt90) cc_final: 0.8021 (mmm-85) REVERT: Y 411 LYS cc_start: 0.8333 (mtpp) cc_final: 0.8121 (mtpt) REVERT: Y 437 ARG cc_start: 0.7591 (mtt-85) cc_final: 0.7208 (mmm-85) REVERT: Y 484 MET cc_start: 0.8248 (tpp) cc_final: 0.7941 (tpt) REVERT: Z 51 ARG cc_start: 0.8906 (ttt90) cc_final: 0.8039 (ttt90) REVERT: Z 82 ASP cc_start: 0.8317 (t0) cc_final: 0.7347 (t0) REVERT: Z 152 GLU cc_start: 0.8530 (tp30) cc_final: 0.8314 (mm-30) REVERT: Z 292 GLN cc_start: 0.8246 (tt0) cc_final: 0.7878 (tt0) REVERT: Z 358 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9031 (mp) REVERT: Z 411 LYS cc_start: 0.8020 (tmmt) cc_final: 0.7599 (mptp) REVERT: Z 484 MET cc_start: 0.7072 (mmm) cc_final: 0.6533 (tmt) REVERT: Z 493 LYS cc_start: 0.7801 (mtmt) cc_final: 0.7422 (mttt) REVERT: Z 573 LYS cc_start: 0.7341 (tppt) cc_final: 0.7018 (ttpt) outliers start: 107 outliers final: 37 residues processed: 522 average time/residue: 0.6576 time to fit residues: 414.3931 Evaluate side-chains 466 residues out of total 3569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 416 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain J residue 92 ASN Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 71 GLN Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain P residue 136 GLU Chi-restraints excluded: chain R residue 126 LYS Chi-restraints excluded: chain R residue 182 ARG Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 86 VAL Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 275 GLU Chi-restraints excluded: chain T residue 183 SER Chi-restraints excluded: chain T residue 279 THR Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 149 GLN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 427 VAL Chi-restraints excluded: chain V residue 449 GLU Chi-restraints excluded: chain V residue 554 LEU Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Z residue 69 SER Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 358 LEU Chi-restraints excluded: chain Z residue 426 SER Chi-restraints excluded: chain Z residue 492 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: [262, 386, 253, 280, 187, 114, 30, 272, 271, 329, 292] chunk 262 optimal weight: 0.1980 chunk 386 optimal weight: 9.9990 chunk 253 optimal weight: 2.9990 chunk 280 optimal weight: 0.3980 chunk 187 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 272 optimal weight: 1.9990 chunk 271 optimal weight: 0.2980 chunk 329 optimal weight: 1.9990 chunk 292 optimal weight: 0.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 98 GLN G 87 ASN J 92 ASN P 83 GLN P 140 ASN ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 529 ASN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 121 ASN V 358 HIS V 515 GLN X 278 GLN ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.145981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.102722 restraints weight = 44592.110| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.71 r_work: 0.3061 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34443 Z= 0.118 Angle : 0.546 10.148 46679 Z= 0.277 Chirality : 0.043 0.163 5526 Planarity : 0.004 0.045 5999 Dihedral : 5.662 105.469 4828 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.45 % Favored : 96.50 % Rotamer: Outliers : 3.48 % Allowed : 17.35 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.13), residues: 4463 helix: -0.35 (0.11), residues: 2183 sheet: -0.65 (0.21), residues: 567 loop : -0.71 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 496 TYR 0.016 0.001 TYR V 414 PHE 0.026 0.001 PHE I 107 TRP 0.007 0.001 TRP R 37 HIS 0.004 0.001 HIS U 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (34443) covalent geometry : angle 0.54610 / 0.28 (46679) hydrogen bonds : bond 0.03498 / 2.31 ( 1596) hydrogen bonds : angle 4.57878 / 3.16 ( 4593) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 3569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 450 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.7697 (mpp) cc_final: 0.7466 (mtm) REVERT: B 107 PHE cc_start: 0.7134 (t80) cc_final: 0.6807 (t80) REVERT: C 69 ILE cc_start: 0.8226 (pt) cc_final: 0.7974 (pp) REVERT: C 97 LYS cc_start: 0.8712 (mppt) cc_final: 0.8421 (mttm) REVERT: D 61 MET cc_start: 0.8009 (mpt) cc_final: 0.7616 (mmt) REVERT: E 60 LYS cc_start: 0.6523 (ptpp) cc_final: 0.6273 (mtmp) REVERT: E 92 ASN cc_start: 0.7667 (p0) cc_final: 0.6844 (p0) REVERT: E 95 ILE cc_start: 0.7812 (mm) cc_final: 0.7588 (mp) REVERT: F 81 MET cc_start: 0.8144 (ttp) cc_final: 0.7831 (ttp) REVERT: F 111 GLU cc_start: 0.8052 (tp30) cc_final: 0.7802 (mm-30) REVERT: G 62 VAL cc_start: 0.7767 (OUTLIER) cc_final: 0.7539 (p) REVERT: G 87 ASN cc_start: 0.7043 (m-40) cc_final: 0.6813 (m-40) REVERT: G 95 ILE cc_start: 0.7953 (mm) cc_final: 0.7678 (mm) REVERT: G 102 TYR cc_start: 0.7140 (m-80) cc_final: 0.6700 (m-80) REVERT: I 119 LEU cc_start: 0.6694 (OUTLIER) cc_final: 0.6181 (pp) REVERT: J 59 SER cc_start: 0.7315 (p) cc_final: 0.6919 (p) REVERT: J 61 MET cc_start: 0.7418 (mpt) cc_final: 0.7120 (mpt) REVERT: J 66 CYS cc_start: 0.8023 (m) cc_final: 0.7559 (m) REVERT: J 71 LEU cc_start: 0.8141 (mp) cc_final: 0.7893 (tp) REVERT: P 49 THR cc_start: 0.8375 (OUTLIER) cc_final: 0.8076 (t) REVERT: P 63 LYS cc_start: 0.8708 (tppt) cc_final: 0.8490 (tptm) REVERT: P 72 ASP cc_start: 0.8106 (t0) cc_final: 0.7905 (t0) REVERT: P 103 LYS cc_start: 0.8557 (mmmm) cc_final: 0.7871 (mmmt) REVERT: P 122 PHE cc_start: 0.8398 (m-80) cc_final: 0.8007 (m-80) REVERT: P 128 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7900 (mm-30) REVERT: P 136 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8299 (tp30) REVERT: P 145 MET cc_start: 0.8675 (mmm) cc_final: 0.8461 (mmm) REVERT: Q 10 ARG cc_start: 0.7529 (tpp-160) cc_final: 0.7255 (ttm-80) REVERT: Q 40 GLN cc_start: 0.7371 (mm-40) cc_final: 0.7027 (tm-30) REVERT: R 127 PHE cc_start: 0.7355 (m-80) cc_final: 0.7147 (m-80) REVERT: R 182 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6937 (ttt180) REVERT: S 68 MET cc_start: 0.8192 (ttp) cc_final: 0.7962 (ttp) REVERT: S 169 ARG cc_start: 0.7979 (ptm160) cc_final: 0.7688 (ptm160) REVERT: S 190 TYR cc_start: 0.8374 (m-80) cc_final: 0.7975 (m-80) REVERT: S 232 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7628 (m-30) REVERT: S 234 GLU cc_start: 0.8096 (tm-30) cc_final: 0.6791 (tm-30) REVERT: S 275 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7460 (tm-30) REVERT: U 71 LYS cc_start: 0.8342 (tppt) cc_final: 0.8090 (tppp) REVERT: U 84 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8970 (mp) REVERT: U 482 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7859 (mm-30) REVERT: U 511 LYS cc_start: 0.7756 (mttt) cc_final: 0.7138 (mttm) REVERT: V 61 HIS cc_start: 0.8137 (t-90) cc_final: 0.7743 (t-170) REVERT: V 67 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8286 (mt) REVERT: V 149 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7774 (mm-40) REVERT: V 455 GLU cc_start: 0.7904 (pt0) cc_final: 0.7452 (pp20) REVERT: X 215 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7860 (mm-30) REVERT: X 471 GLN cc_start: 0.8145 (tt0) cc_final: 0.7766 (tp-100) REVERT: X 573 LYS cc_start: 0.7475 (mtmt) cc_final: 0.7270 (mtpt) REVERT: Y 385 ARG cc_start: 0.8296 (mmt90) cc_final: 0.7984 (mmm-85) REVERT: Y 437 ARG cc_start: 0.7663 (mtt-85) cc_final: 0.7301 (mmm-85) REVERT: Y 484 MET cc_start: 0.8215 (tpp) cc_final: 0.7904 (tpt) REVERT: Z 152 GLU cc_start: 0.8537 (tp30) cc_final: 0.8320 (mm-30) REVERT: Z 292 GLN cc_start: 0.8240 (tt0) cc_final: 0.7884 (tt0) REVERT: Z 411 LYS cc_start: 0.7968 (tmmt) cc_final: 0.7570 (mptp) REVERT: Z 441 ARG cc_start: 0.7755 (mmt-90) cc_final: 0.7422 (mmt-90) REVERT: Z 484 MET cc_start: 0.7123 (mmm) cc_final: 0.6550 (tmt) REVERT: Z 493 LYS cc_start: 0.7657 (mtmt) cc_final: 0.7339 (mttt) REVERT: Z 573 LYS cc_start: 0.7345 (tppt) cc_final: 0.7009 (ttmt) outliers start: 124 outliers final: 46 residues processed: 527 average time/residue: 0.6222 time to fit residues: 399.2798 Evaluate side-chains 478 residues out of total 3569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 422 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain P residue 136 GLU Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 126 LYS Chi-restraints excluded: chain R residue 182 ARG Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 86 VAL Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 232 ASP Chi-restraints excluded: chain S residue 275 GLU Chi-restraints excluded: chain T residue 103 VAL Chi-restraints excluded: chain T residue 183 SER Chi-restraints excluded: chain T residue 279 THR Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 149 GLN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 427 VAL Chi-restraints excluded: chain V residue 465 ASP Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 415 ASP Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Z residue 69 SER Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 426 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: [52, 439, 346, 327, 83, 395, 406, 270, 155, 15, 1] chunk 52 optimal weight: 2.9990 chunk 439 optimal weight: 10.0000 chunk 346 optimal weight: 3.9990 chunk 327 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 395 optimal weight: 2.9990 chunk 406 optimal weight: 0.8980 chunk 270 optimal weight: 0.0980 chunk 155 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 98 GLN J 92 ASN P 83 GLN P 140 ASN ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 435 GLN T 529 ASN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 440 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.145604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.103233 restraints weight = 44663.031| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.77 r_work: 0.3050 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34443 Z= 0.127 Angle : 0.545 8.937 46679 Z= 0.277 Chirality : 0.043 0.179 5526 Planarity : 0.004 0.046 5999 Dihedral : 5.532 103.717 4827 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.56 % Favored : 96.39 % Rotamer: Outliers : 3.45 % Allowed : 18.05 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.13), residues: 4463 helix: -0.04 (0.11), residues: 2193 sheet: -0.59 (0.22), residues: 567 loop : -0.61 (0.16), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG T 496 TYR 0.014 0.001 TYR V 414 PHE 0.027 0.001 PHE A 107 TRP 0.008 0.001 TRP R 37 HIS 0.003 0.001 HIS S 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (34443) covalent geometry : angle 0.54521 / 0.28 (46679) hydrogen bonds : bond 0.03462 / 2.29 ( 1596) hydrogen bonds : angle 4.48473 / 3.10 ( 4593) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 444 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.7551 (mpp) cc_final: 0.7326 (mtm) REVERT: C 69 ILE cc_start: 0.8167 (pt) cc_final: 0.7916 (pp) REVERT: D 61 MET cc_start: 0.7978 (mpt) cc_final: 0.7659 (mmt) REVERT: E 60 LYS cc_start: 0.6529 (ptpp) cc_final: 0.6079 (mtmm) REVERT: E 95 ILE cc_start: 0.7759 (mm) cc_final: 0.7465 (mp) REVERT: F 81 MET cc_start: 0.8125 (ttp) cc_final: 0.7723 (ttp) REVERT: F 111 GLU cc_start: 0.8045 (tp30) cc_final: 0.7811 (mm-30) REVERT: G 62 VAL cc_start: 0.7715 (OUTLIER) cc_final: 0.7491 (p) REVERT: G 87 ASN cc_start: 0.7083 (m-40) cc_final: 0.6869 (m-40) REVERT: G 95 ILE cc_start: 0.7835 (mm) cc_final: 0.7588 (mm) REVERT: G 102 TYR cc_start: 0.7092 (m-80) cc_final: 0.6740 (m-80) REVERT: I 98 GLN cc_start: 0.7494 (tm-30) cc_final: 0.7283 (tm-30) REVERT: I 119 LEU cc_start: 0.6594 (OUTLIER) cc_final: 0.6115 (pp) REVERT: J 59 SER cc_start: 0.7310 (p) cc_final: 0.6932 (p) REVERT: J 61 MET cc_start: 0.7427 (mpt) cc_final: 0.7109 (mpt) REVERT: J 66 CYS cc_start: 0.8061 (m) cc_final: 0.7585 (m) REVERT: P 49 THR cc_start: 0.8397 (OUTLIER) cc_final: 0.8097 (t) REVERT: P 63 LYS cc_start: 0.8707 (tppt) cc_final: 0.8479 (tptm) REVERT: P 103 LYS cc_start: 0.8432 (mmmm) cc_final: 0.7791 (mmmt) REVERT: P 122 PHE cc_start: 0.8430 (m-80) cc_final: 0.8043 (m-80) REVERT: P 136 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8229 (tp30) REVERT: Q 10 ARG cc_start: 0.7622 (tpp-160) cc_final: 0.7212 (ttm-80) REVERT: Q 40 GLN cc_start: 0.7247 (mm-40) cc_final: 0.6995 (tm-30) REVERT: R 127 PHE cc_start: 0.7308 (m-80) cc_final: 0.7094 (m-80) REVERT: S 190 TYR cc_start: 0.8317 (m-80) cc_final: 0.7954 (m-80) REVERT: S 232 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7624 (m-30) REVERT: S 234 GLU cc_start: 0.8065 (tm-30) cc_final: 0.6760 (tm-30) REVERT: S 266 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8635 (tt0) REVERT: S 275 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7540 (tm-30) REVERT: U 71 LYS cc_start: 0.8381 (tppt) cc_final: 0.8119 (tppp) REVERT: U 84 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8934 (mp) REVERT: U 282 MET cc_start: 0.9238 (tpt) cc_final: 0.8828 (tpt) REVERT: U 482 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7854 (mm-30) REVERT: V 67 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8269 (mt) REVERT: V 149 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7764 (mm-40) REVERT: V 449 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7457 (mt-10) REVERT: V 455 GLU cc_start: 0.8005 (pt0) cc_final: 0.7607 (pp20) REVERT: X 215 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7898 (mm-30) REVERT: X 430 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7943 (ttmt) REVERT: X 471 GLN cc_start: 0.8161 (tt0) cc_final: 0.7807 (tp-100) REVERT: X 573 LYS cc_start: 0.7436 (mtmt) cc_final: 0.7203 (mtpt) REVERT: Y 51 ARG cc_start: 0.8739 (ttt-90) cc_final: 0.8366 (ttt-90) REVERT: Y 243 LYS cc_start: 0.8785 (mtpt) cc_final: 0.8116 (mmtm) REVERT: Y 385 ARG cc_start: 0.8287 (mmt90) cc_final: 0.7983 (mmm-85) REVERT: Y 437 ARG cc_start: 0.7681 (mtt-85) cc_final: 0.7218 (mmm-85) REVERT: Y 484 MET cc_start: 0.8237 (tpp) cc_final: 0.7947 (tpt) REVERT: Z 51 ARG cc_start: 0.8952 (ttt90) cc_final: 0.8084 (ttt90) REVERT: Z 82 ASP cc_start: 0.8329 (t0) cc_final: 0.7300 (t0) REVERT: Z 152 GLU cc_start: 0.8554 (tp30) cc_final: 0.8332 (mm-30) REVERT: Z 292 GLN cc_start: 0.8258 (tt0) cc_final: 0.7913 (tt0) REVERT: Z 411 LYS cc_start: 0.8021 (tmmt) cc_final: 0.7511 (mptp) REVERT: Z 484 MET cc_start: 0.7280 (mmm) cc_final: 0.6667 (tmt) REVERT: Z 493 LYS cc_start: 0.7638 (mtmt) cc_final: 0.7301 (mttt) REVERT: Z 573 LYS cc_start: 0.7335 (tppt) cc_final: 0.6845 (ttmm) outliers start: 123 outliers final: 52 residues processed: 520 average time/residue: 0.6373 time to fit residues: 400.0037 Evaluate side-chains 489 residues out of total 3569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 425 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain P residue 136 GLU Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 126 LYS Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 232 ASP Chi-restraints excluded: chain S residue 266 GLU Chi-restraints excluded: chain S residue 275 GLU Chi-restraints excluded: chain T residue 103 VAL Chi-restraints excluded: chain T residue 183 SER Chi-restraints excluded: chain T residue 237 ASP Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain T residue 279 THR Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 149 GLN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 427 VAL Chi-restraints excluded: chain V residue 448 LEU Chi-restraints excluded: chain V residue 449 GLU Chi-restraints excluded: chain V residue 465 ASP Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 415 ASP Chi-restraints excluded: chain X residue 430 LYS Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 414 GLN Chi-restraints excluded: chain Z residue 69 SER Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain Z residue 426 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: [119, 374, 320, 31, 351, 346, 376, 103, 125, 84, 388] chunk 119 optimal weight: 2.9990 chunk 374 optimal weight: 6.9990 chunk 320 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 351 optimal weight: 0.6980 chunk 346 optimal weight: 3.9990 chunk 376 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 388 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 92 ASN E 98 GLN F 98 GLN J 92 ASN P 52 GLN P 83 GLN Q 21 ASN ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 529 ASN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN V 515 GLN Y 83 ASN ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 440 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.144137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.100372 restraints weight = 44426.382| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.60 r_work: 0.3051 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 34443 Z= 0.160 Angle : 0.572 11.228 46679 Z= 0.290 Chirality : 0.045 0.262 5526 Planarity : 0.004 0.048 5999 Dihedral : 5.613 102.159 4827 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.61 % Favored : 96.35 % Rotamer: Outliers : 3.62 % Allowed : 18.75 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.13), residues: 4463 helix: 0.06 (0.11), residues: 2211 sheet: -0.66 (0.21), residues: 591 loop : -0.57 (0.16), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 496 TYR 0.013 0.001 TYR V 414 PHE 0.037 0.002 PHE A 107 TRP 0.010 0.001 TRP R 37 HIS 0.004 0.001 HIS S 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (34443) covalent geometry : angle 0.57190 / 0.29 (46679) hydrogen bonds : bond 0.03627 / 2.39 ( 1596) hydrogen bonds : angle 4.52500 / 3.12 ( 4593) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 3569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 440 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 107 PHE cc_start: 0.7286 (t80) cc_final: 0.6966 (t80) REVERT: C 69 ILE cc_start: 0.8223 (pt) cc_final: 0.7990 (pp) REVERT: C 85 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.8018 (tt) REVERT: C 97 LYS cc_start: 0.8752 (mppt) cc_final: 0.8451 (mttm) REVERT: D 61 MET cc_start: 0.8029 (mpt) cc_final: 0.7727 (mmt) REVERT: D 113 ILE cc_start: 0.5389 (OUTLIER) cc_final: 0.4791 (mp) REVERT: E 60 LYS cc_start: 0.6655 (ptpp) cc_final: 0.6142 (mtmm) REVERT: E 95 ILE cc_start: 0.7758 (mm) cc_final: 0.7546 (mp) REVERT: F 81 MET cc_start: 0.8142 (ttp) cc_final: 0.7810 (ttp) REVERT: F 111 GLU cc_start: 0.8041 (tp30) cc_final: 0.7823 (mm-30) REVERT: G 62 VAL cc_start: 0.7806 (OUTLIER) cc_final: 0.7582 (p) REVERT: G 87 ASN cc_start: 0.7213 (m-40) cc_final: 0.7008 (m-40) REVERT: G 95 ILE cc_start: 0.7884 (mm) cc_final: 0.7644 (mm) REVERT: G 102 TYR cc_start: 0.7069 (m-80) cc_final: 0.6746 (m-80) REVERT: I 98 GLN cc_start: 0.7573 (tm-30) cc_final: 0.7271 (tm-30) REVERT: I 119 LEU cc_start: 0.6450 (OUTLIER) cc_final: 0.6064 (pp) REVERT: J 59 SER cc_start: 0.7363 (p) cc_final: 0.6990 (p) REVERT: J 61 MET cc_start: 0.7487 (mpt) cc_final: 0.7152 (mpt) REVERT: J 66 CYS cc_start: 0.8064 (m) cc_final: 0.7610 (m) REVERT: P 49 THR cc_start: 0.8392 (OUTLIER) cc_final: 0.8111 (t) REVERT: P 63 LYS cc_start: 0.8725 (tppt) cc_final: 0.8500 (tptm) REVERT: P 103 LYS cc_start: 0.8489 (mmmm) cc_final: 0.7857 (mmmt) REVERT: P 128 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7851 (mm-30) REVERT: P 136 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8221 (tp30) REVERT: Q 10 ARG cc_start: 0.7706 (tpp-160) cc_final: 0.7330 (ttm-80) REVERT: Q 40 GLN cc_start: 0.7294 (mm-40) cc_final: 0.7066 (tm-30) REVERT: S 169 ARG cc_start: 0.8019 (ptm160) cc_final: 0.7793 (ptp90) REVERT: S 190 TYR cc_start: 0.8434 (m-80) cc_final: 0.8105 (m-80) REVERT: S 232 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7646 (m-30) REVERT: S 234 GLU cc_start: 0.8105 (tm-30) cc_final: 0.6838 (tm-30) REVERT: S 266 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8637 (tt0) REVERT: S 275 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7647 (tm-30) REVERT: T 448 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7804 (tp) REVERT: U 71 LYS cc_start: 0.8412 (tppt) cc_final: 0.8155 (tppp) REVERT: U 84 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8950 (mp) REVERT: U 391 SER cc_start: 0.9052 (p) cc_final: 0.8744 (m) REVERT: U 482 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7862 (mm-30) REVERT: V 61 HIS cc_start: 0.8048 (t-170) cc_final: 0.7768 (t-170) REVERT: V 149 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7796 (mm-40) REVERT: V 455 GLU cc_start: 0.8006 (pt0) cc_final: 0.7621 (pp20) REVERT: X 215 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7867 (mm-30) REVERT: X 430 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7998 (ttmt) REVERT: X 573 LYS cc_start: 0.7495 (mtmt) cc_final: 0.7269 (mtpt) REVERT: Y 149 GLU cc_start: 0.6676 (OUTLIER) cc_final: 0.6449 (mp0) REVERT: Y 239 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.6904 (tmm160) REVERT: Y 243 LYS cc_start: 0.8789 (mtpt) cc_final: 0.8136 (mmtm) REVERT: Y 385 ARG cc_start: 0.8296 (mmt90) cc_final: 0.7991 (mmm-85) REVERT: Y 401 ARG cc_start: 0.7744 (mmm160) cc_final: 0.6782 (mmt180) REVERT: Y 437 ARG cc_start: 0.7683 (mtt-85) cc_final: 0.7214 (mmm-85) REVERT: Y 484 MET cc_start: 0.8281 (tpp) cc_final: 0.8016 (tpt) REVERT: Z 152 GLU cc_start: 0.8572 (tp30) cc_final: 0.8349 (mm-30) REVERT: Z 292 GLN cc_start: 0.8310 (tt0) cc_final: 0.7973 (tt0) REVERT: Z 411 LYS cc_start: 0.8032 (tmmt) cc_final: 0.7568 (mptp) REVERT: Z 484 MET cc_start: 0.7287 (mmm) cc_final: 0.6549 (tpp) REVERT: Z 493 LYS cc_start: 0.7626 (mtmt) cc_final: 0.7367 (mttt) REVERT: Z 573 LYS cc_start: 0.7423 (tppt) cc_final: 0.6882 (ttmm) outliers start: 129 outliers final: 65 residues processed: 526 average time/residue: 0.6367 time to fit residues: 406.8804 Evaluate side-chains 505 residues out of total 3569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 425 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain P residue 136 GLU Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 126 LYS Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 86 VAL Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 232 ASP Chi-restraints excluded: chain S residue 266 GLU Chi-restraints excluded: chain S residue 275 GLU Chi-restraints excluded: chain T residue 103 VAL Chi-restraints excluded: chain T residue 183 SER Chi-restraints excluded: chain T residue 237 ASP Chi-restraints excluded: chain T residue 279 THR Chi-restraints excluded: chain T residue 448 LEU Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain T residue 556 LYS Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 149 GLN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 427 VAL Chi-restraints excluded: chain V residue 442 VAL Chi-restraints excluded: chain V residue 448 LEU Chi-restraints excluded: chain V residue 465 ASP Chi-restraints excluded: chain V residue 481 THR Chi-restraints excluded: chain V residue 516 ASP Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 415 ASP Chi-restraints excluded: chain X residue 430 LYS Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain Y residue 149 GLU Chi-restraints excluded: chain Y residue 239 ARG Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 414 GLN Chi-restraints excluded: chain Y residue 452 VAL Chi-restraints excluded: chain Z residue 69 SER Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain Z residue 426 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: [57, 110, 436, 269, 25, 200, 215, 263, 386, 207, 412] chunk 57 optimal weight: 0.0970 chunk 110 optimal weight: 0.3980 chunk 436 optimal weight: 0.9990 chunk 269 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 200 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 263 optimal weight: 0.9980 chunk 386 optimal weight: 9.9990 chunk 207 optimal weight: 0.7980 chunk 412 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 98 GLN J 98 GLN P 83 GLN ** Q 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 241 HIS T 435 GLN T 529 ASN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN V 219 GLN V 515 GLN Y 83 ASN ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.145921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.102471 restraints weight = 44808.722| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.61 r_work: 0.3079 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34443 Z= 0.117 Angle : 0.548 10.508 46679 Z= 0.277 Chirality : 0.043 0.242 5526 Planarity : 0.004 0.049 5999 Dihedral : 5.451 103.553 4827 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.41 % Favored : 96.55 % Rotamer: Outliers : 3.25 % Allowed : 19.56 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.13), residues: 4463 helix: 0.26 (0.11), residues: 2215 sheet: -0.53 (0.22), residues: 567 loop : -0.49 (0.16), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG T 199 TYR 0.015 0.001 TYR V 414 PHE 0.034 0.001 PHE A 107 TRP 0.007 0.001 TRP R 37 HIS 0.003 0.001 HIS S 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (34443) covalent geometry : angle 0.54763 / 0.28 (46679) hydrogen bonds : bond 0.03298 / 2.18 ( 1596) hydrogen bonds : angle 4.41674 / 3.05 ( 4593) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 437 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 PHE cc_start: 0.7171 (m-80) cc_final: 0.6947 (m-80) REVERT: C 69 ILE cc_start: 0.8188 (pt) cc_final: 0.7956 (pp) REVERT: C 81 MET cc_start: 0.8088 (tpp) cc_final: 0.7565 (ttt) REVERT: C 85 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7994 (tt) REVERT: D 61 MET cc_start: 0.7913 (mpt) cc_final: 0.7659 (mmt) REVERT: D 113 ILE cc_start: 0.5258 (OUTLIER) cc_final: 0.4682 (mp) REVERT: F 81 MET cc_start: 0.8075 (ttp) cc_final: 0.7762 (ttp) REVERT: F 111 GLU cc_start: 0.8106 (tp30) cc_final: 0.7850 (mm-30) REVERT: G 62 VAL cc_start: 0.7658 (OUTLIER) cc_final: 0.7436 (p) REVERT: G 95 ILE cc_start: 0.7859 (mm) cc_final: 0.7626 (mm) REVERT: G 102 TYR cc_start: 0.7239 (m-10) cc_final: 0.6693 (m-80) REVERT: I 98 GLN cc_start: 0.7537 (tm-30) cc_final: 0.7197 (tm-30) REVERT: I 119 LEU cc_start: 0.6485 (OUTLIER) cc_final: 0.6089 (pp) REVERT: J 59 SER cc_start: 0.7383 (p) cc_final: 0.7120 (p) REVERT: J 61 MET cc_start: 0.7456 (mpt) cc_final: 0.7190 (mpt) REVERT: J 66 CYS cc_start: 0.8109 (m) cc_final: 0.7646 (m) REVERT: J 107 PHE cc_start: 0.6795 (t80) cc_final: 0.6322 (t80) REVERT: P 49 THR cc_start: 0.8355 (OUTLIER) cc_final: 0.8064 (t) REVERT: P 63 LYS cc_start: 0.8725 (tppt) cc_final: 0.8495 (tptm) REVERT: P 73 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7992 (mt-10) REVERT: P 103 LYS cc_start: 0.8422 (mmmm) cc_final: 0.7837 (mmmt) REVERT: P 122 PHE cc_start: 0.8664 (m-80) cc_final: 0.8264 (m-80) REVERT: P 128 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7915 (mm-30) REVERT: P 134 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8578 (tp) REVERT: P 136 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8224 (tp30) REVERT: Q 10 ARG cc_start: 0.7750 (tpp-160) cc_final: 0.7319 (ttm-80) REVERT: Q 21 ASN cc_start: 0.8590 (m-40) cc_final: 0.8214 (m110) REVERT: Q 40 GLN cc_start: 0.7316 (mm-40) cc_final: 0.7038 (tm-30) REVERT: S 190 TYR cc_start: 0.8352 (m-80) cc_final: 0.8031 (m-80) REVERT: S 232 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7652 (m-30) REVERT: S 234 GLU cc_start: 0.8008 (tm-30) cc_final: 0.6783 (tm-30) REVERT: S 266 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8606 (tt0) REVERT: S 275 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7648 (tm-30) REVERT: U 71 LYS cc_start: 0.8404 (tppt) cc_final: 0.8101 (tppp) REVERT: U 84 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8968 (mp) REVERT: U 482 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7804 (mm-30) REVERT: V 61 HIS cc_start: 0.8037 (t-170) cc_final: 0.7704 (t-170) REVERT: V 67 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8294 (mt) REVERT: V 149 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7749 (mm-40) REVERT: V 455 GLU cc_start: 0.8017 (pt0) cc_final: 0.7627 (pp20) REVERT: X 215 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7883 (mm-30) REVERT: Y 51 ARG cc_start: 0.8726 (ttt-90) cc_final: 0.8377 (ttt-90) REVERT: Y 149 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.6454 (mp0) REVERT: Y 243 LYS cc_start: 0.8778 (mtpt) cc_final: 0.8135 (mmtm) REVERT: Y 385 ARG cc_start: 0.8280 (mmt90) cc_final: 0.7986 (mmm-85) REVERT: Y 411 LYS cc_start: 0.8269 (mtpp) cc_final: 0.7965 (ttpt) REVERT: Y 437 ARG cc_start: 0.7741 (mtt-85) cc_final: 0.7275 (mmm-85) REVERT: Y 484 MET cc_start: 0.8307 (tpp) cc_final: 0.8107 (tpt) REVERT: Z 51 ARG cc_start: 0.8942 (ttt90) cc_final: 0.8353 (ttt90) REVERT: Z 82 ASP cc_start: 0.8336 (t0) cc_final: 0.7623 (t0) REVERT: Z 152 GLU cc_start: 0.8581 (tp30) cc_final: 0.8367 (mm-30) REVERT: Z 292 GLN cc_start: 0.8274 (tt0) cc_final: 0.7959 (tt0) REVERT: Z 411 LYS cc_start: 0.8007 (tmmt) cc_final: 0.7536 (mptp) REVERT: Z 426 SER cc_start: 0.6987 (OUTLIER) cc_final: 0.6481 (p) REVERT: Z 484 MET cc_start: 0.7140 (mmm) cc_final: 0.6450 (tpp) REVERT: Z 493 LYS cc_start: 0.7619 (mtmt) cc_final: 0.7341 (mttt) REVERT: Z 535 LYS cc_start: 0.7653 (mtpt) cc_final: 0.6790 (mmmt) REVERT: Z 573 LYS cc_start: 0.7426 (tppt) cc_final: 0.6864 (ttmm) outliers start: 116 outliers final: 64 residues processed: 516 average time/residue: 0.6142 time to fit residues: 385.7339 Evaluate side-chains 487 residues out of total 3569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 408 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain P residue 136 GLU Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 126 LYS Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain S residue 86 VAL Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 232 ASP Chi-restraints excluded: chain S residue 266 GLU Chi-restraints excluded: chain S residue 275 GLU Chi-restraints excluded: chain S residue 304 LEU Chi-restraints excluded: chain T residue 103 VAL Chi-restraints excluded: chain T residue 183 SER Chi-restraints excluded: chain T residue 237 ASP Chi-restraints excluded: chain T residue 279 THR Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 149 GLN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 427 VAL Chi-restraints excluded: chain V residue 442 VAL Chi-restraints excluded: chain V residue 448 LEU Chi-restraints excluded: chain V residue 465 ASP Chi-restraints excluded: chain V residue 515 GLN Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 415 ASP Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 468 SER Chi-restraints excluded: chain Y residue 149 GLU Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Z residue 69 SER Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain Z residue 426 SER Chi-restraints excluded: chain Z residue 528 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: [38, 212, 434, 214, 173, 200, 247, 339, 259, 240, 297] chunk 38 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 chunk 434 optimal weight: 0.0270 chunk 214 optimal weight: 1.9990 chunk 173 optimal weight: 0.2980 chunk 200 optimal weight: 0.9990 chunk 247 optimal weight: 4.9990 chunk 339 optimal weight: 3.9990 chunk 259 optimal weight: 2.9990 chunk 240 optimal weight: 2.9990 chunk 297 optimal weight: 1.9990 overall best weight: 1.0644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 92 ASN E 98 GLN P 52 GLN ** Q 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 169 GLN ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 529 ASN U 497 GLN U 539 ASN V 515 GLN Y 83 ASN Z 286 ASN Z 440 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.144351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.100682 restraints weight = 44645.297| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.60 r_work: 0.3052 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 34443 Z= 0.160 Angle : 0.584 14.325 46679 Z= 0.294 Chirality : 0.045 0.279 5526 Planarity : 0.004 0.053 5999 Dihedral : 5.532 101.112 4827 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.72 % Favored : 96.26 % Rotamer: Outliers : 3.50 % Allowed : 19.51 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.13), residues: 4463 helix: 0.27 (0.11), residues: 2214 sheet: -0.59 (0.21), residues: 594 loop : -0.51 (0.16), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG T 199 TYR 0.021 0.001 TYR T 502 PHE 0.044 0.002 PHE E 107 TRP 0.010 0.001 TRP R 37 HIS 0.004 0.001 HIS S 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (34443) covalent geometry : angle 0.58392 / 0.29 (46679) hydrogen bonds : bond 0.03557 / 2.35 ( 1596) hydrogen bonds : angle 4.47845 / 3.09 ( 4593) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 3569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 426 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 PHE cc_start: 0.7209 (t80) cc_final: 0.6854 (t80) REVERT: C 69 ILE cc_start: 0.8153 (pt) cc_final: 0.7946 (pp) REVERT: C 81 MET cc_start: 0.8036 (tpp) cc_final: 0.7519 (ttt) REVERT: C 85 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.8039 (tt) REVERT: D 61 MET cc_start: 0.7910 (mpt) cc_final: 0.7664 (mmt) REVERT: E 95 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7648 (mp) REVERT: E 98 GLN cc_start: 0.7041 (OUTLIER) cc_final: 0.6832 (tm-30) REVERT: F 111 GLU cc_start: 0.8098 (tp30) cc_final: 0.7873 (mm-30) REVERT: G 62 VAL cc_start: 0.7668 (OUTLIER) cc_final: 0.7454 (p) REVERT: G 95 ILE cc_start: 0.7866 (mm) cc_final: 0.7643 (mm) REVERT: G 102 TYR cc_start: 0.7267 (m-10) cc_final: 0.6779 (m-80) REVERT: I 98 GLN cc_start: 0.7482 (tm-30) cc_final: 0.7247 (tm-30) REVERT: I 99 LEU cc_start: 0.6739 (OUTLIER) cc_final: 0.6218 (mp) REVERT: I 119 LEU cc_start: 0.6563 (OUTLIER) cc_final: 0.6208 (pp) REVERT: J 59 SER cc_start: 0.7308 (p) cc_final: 0.7048 (p) REVERT: J 61 MET cc_start: 0.7480 (mpt) cc_final: 0.7205 (mpt) REVERT: J 66 CYS cc_start: 0.8079 (m) cc_final: 0.7645 (m) REVERT: P 49 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.8103 (t) REVERT: P 63 LYS cc_start: 0.8720 (tppt) cc_final: 0.8483 (tptm) REVERT: P 72 ASP cc_start: 0.7842 (t0) cc_final: 0.7252 (t70) REVERT: P 73 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7994 (mt-10) REVERT: P 128 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7885 (mm-30) REVERT: P 136 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8249 (tp30) REVERT: Q 10 ARG cc_start: 0.7785 (tpp-160) cc_final: 0.7289 (ttm-80) REVERT: Q 21 ASN cc_start: 0.8621 (m-40) cc_final: 0.8237 (m110) REVERT: Q 40 GLN cc_start: 0.7246 (mm-40) cc_final: 0.6856 (tp-100) REVERT: R 35 GLU cc_start: 0.6717 (OUTLIER) cc_final: 0.6213 (mm-30) REVERT: S 68 MET cc_start: 0.8060 (ttp) cc_final: 0.7859 (ttp) REVERT: S 190 TYR cc_start: 0.8407 (m-80) cc_final: 0.8068 (m-80) REVERT: S 232 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7582 (m-30) REVERT: S 234 GLU cc_start: 0.8061 (tm-30) cc_final: 0.6824 (tm-30) REVERT: S 266 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8646 (tt0) REVERT: S 275 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7693 (tm-30) REVERT: T 447 LYS cc_start: 0.7984 (ptpt) cc_final: 0.7739 (ptpp) REVERT: U 71 LYS cc_start: 0.8408 (tppt) cc_final: 0.8103 (tppp) REVERT: U 84 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8989 (mp) REVERT: V 61 HIS cc_start: 0.8078 (t-170) cc_final: 0.7674 (t-170) REVERT: V 67 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8317 (mt) REVERT: V 149 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7793 (mm-40) REVERT: V 455 GLU cc_start: 0.8008 (pt0) cc_final: 0.7621 (pp20) REVERT: X 215 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7958 (mm-30) REVERT: X 430 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.7996 (ttmt) REVERT: Y 51 ARG cc_start: 0.8757 (ttt-90) cc_final: 0.8397 (ttt-90) REVERT: Y 149 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.6380 (mp0) REVERT: Y 243 LYS cc_start: 0.8794 (mtpt) cc_final: 0.8144 (mmtm) REVERT: Y 385 ARG cc_start: 0.8306 (mmt90) cc_final: 0.8008 (mmm-85) REVERT: Y 411 LYS cc_start: 0.8280 (mtpp) cc_final: 0.7974 (ttpt) REVERT: Y 437 ARG cc_start: 0.7678 (mtt-85) cc_final: 0.7209 (mmm-85) REVERT: Y 484 MET cc_start: 0.8316 (tpp) cc_final: 0.8001 (tpt) REVERT: Z 152 GLU cc_start: 0.8591 (tp30) cc_final: 0.8374 (mm-30) REVERT: Z 292 GLN cc_start: 0.8306 (tt0) cc_final: 0.7967 (tt0) REVERT: Z 411 LYS cc_start: 0.8013 (tmmt) cc_final: 0.7451 (mptp) REVERT: Z 484 MET cc_start: 0.7236 (mmm) cc_final: 0.6544 (tpp) REVERT: Z 493 LYS cc_start: 0.7607 (mtmt) cc_final: 0.7326 (mttt) REVERT: Z 535 LYS cc_start: 0.7713 (mtpt) cc_final: 0.6828 (mmmt) outliers start: 125 outliers final: 64 residues processed: 507 average time/residue: 0.6168 time to fit residues: 382.1965 Evaluate side-chains 493 residues out of total 3569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 412 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain H residue 95 ILE Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain P residue 136 GLU Chi-restraints excluded: chain R residue 35 GLU Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 126 LYS Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 86 VAL Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 232 ASP Chi-restraints excluded: chain S residue 266 GLU Chi-restraints excluded: chain S residue 275 GLU Chi-restraints excluded: chain T residue 103 VAL Chi-restraints excluded: chain T residue 183 SER Chi-restraints excluded: chain T residue 202 LEU Chi-restraints excluded: chain T residue 279 THR Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain T residue 556 LYS Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 149 GLN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 427 VAL Chi-restraints excluded: chain V residue 442 VAL Chi-restraints excluded: chain V residue 448 LEU Chi-restraints excluded: chain V residue 465 ASP Chi-restraints excluded: chain V residue 512 VAL Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 415 ASP Chi-restraints excluded: chain X residue 430 LYS Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 468 SER Chi-restraints excluded: chain Y residue 149 GLU Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 452 VAL Chi-restraints excluded: chain Z residue 69 SER Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain Z residue 426 SER Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 528 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: [159, 385, 324, 69, 82, 58, 413, 204, 140, 147, 424] chunk 159 optimal weight: 0.3980 chunk 385 optimal weight: 2.9990 chunk 324 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 413 optimal weight: 0.9990 chunk 204 optimal weight: 0.6980 chunk 140 optimal weight: 0.9980 chunk 147 optimal weight: 0.7980 chunk 424 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 98 GLN F 98 GLN J 92 ASN P 52 GLN ** Q 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 529 ASN U 497 GLN U 539 ASN V 515 GLN Y 83 ASN ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 440 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.145078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.101580 restraints weight = 44617.891| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.61 r_work: 0.3051 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34443 Z= 0.134 Angle : 0.575 11.680 46679 Z= 0.289 Chirality : 0.044 0.254 5526 Planarity : 0.004 0.050 5999 Dihedral : 5.487 102.370 4827 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.54 % Favored : 96.44 % Rotamer: Outliers : 2.97 % Allowed : 20.38 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.13), residues: 4463 helix: 0.37 (0.11), residues: 2199 sheet: -0.48 (0.22), residues: 567 loop : -0.45 (0.16), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG T 199 TYR 0.019 0.001 TYR T 502 PHE 0.048 0.002 PHE E 107 TRP 0.008 0.001 TRP R 37 HIS 0.003 0.001 HIS Z 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (34443) covalent geometry : angle 0.57521 / 0.29 (46679) hydrogen bonds : bond 0.03411 / 2.25 ( 1596) hydrogen bonds : angle 4.45667 / 3.07 ( 4593) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 3569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 421 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 107 PHE cc_start: 0.7265 (t80) cc_final: 0.6894 (t80) REVERT: B 122 PHE cc_start: 0.7163 (m-80) cc_final: 0.6904 (m-80) REVERT: C 69 ILE cc_start: 0.8140 (pt) cc_final: 0.7786 (pp) REVERT: C 81 MET cc_start: 0.8041 (tpp) cc_final: 0.7527 (ttm) REVERT: D 61 MET cc_start: 0.7906 (mpt) cc_final: 0.7673 (mmt) REVERT: E 95 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7685 (mp) REVERT: F 111 GLU cc_start: 0.8105 (tp30) cc_final: 0.7881 (mm-30) REVERT: G 62 VAL cc_start: 0.7550 (OUTLIER) cc_final: 0.7338 (p) REVERT: G 95 ILE cc_start: 0.7857 (mm) cc_final: 0.7636 (mm) REVERT: G 102 TYR cc_start: 0.7247 (m-10) cc_final: 0.6754 (m-80) REVERT: I 98 GLN cc_start: 0.7550 (tm-30) cc_final: 0.7251 (tm-30) REVERT: I 99 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6337 (mp) REVERT: I 119 LEU cc_start: 0.6536 (OUTLIER) cc_final: 0.6237 (pp) REVERT: J 66 CYS cc_start: 0.8175 (m) cc_final: 0.7690 (m) REVERT: P 49 THR cc_start: 0.8398 (OUTLIER) cc_final: 0.8104 (t) REVERT: P 63 LYS cc_start: 0.8710 (tppt) cc_final: 0.8451 (tptm) REVERT: P 72 ASP cc_start: 0.7829 (t0) cc_final: 0.7217 (t70) REVERT: P 73 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7994 (mt-10) REVERT: P 122 PHE cc_start: 0.8652 (m-80) cc_final: 0.8304 (m-80) REVERT: P 128 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7935 (mm-30) REVERT: P 134 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8580 (tp) REVERT: P 136 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8210 (tp30) REVERT: Q 10 ARG cc_start: 0.7744 (tpp-160) cc_final: 0.7227 (ttm-80) REVERT: Q 21 ASN cc_start: 0.8575 (m-40) cc_final: 0.8205 (m110) REVERT: Q 40 GLN cc_start: 0.7163 (mm-40) cc_final: 0.6793 (tp-100) REVERT: R 35 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6162 (mm-30) REVERT: S 190 TYR cc_start: 0.8344 (m-80) cc_final: 0.7998 (m-80) REVERT: S 203 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7762 (m-80) REVERT: S 232 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7566 (m-30) REVERT: S 234 GLU cc_start: 0.8039 (tm-30) cc_final: 0.6803 (tm-30) REVERT: S 266 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8616 (tt0) REVERT: S 275 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7650 (tm-30) REVERT: T 447 LYS cc_start: 0.7937 (ptpt) cc_final: 0.7662 (ptpp) REVERT: U 71 LYS cc_start: 0.8371 (tppt) cc_final: 0.8054 (tppp) REVERT: U 84 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8976 (mp) REVERT: V 61 HIS cc_start: 0.8068 (t-170) cc_final: 0.7626 (t-170) REVERT: V 67 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8295 (mt) REVERT: V 134 ASN cc_start: 0.8524 (p0) cc_final: 0.8043 (t0) REVERT: V 149 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7727 (mm-40) REVERT: V 455 GLU cc_start: 0.8022 (pt0) cc_final: 0.7608 (pp20) REVERT: X 215 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7971 (mm-30) REVERT: X 430 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7960 (ttmt) REVERT: Y 51 ARG cc_start: 0.8756 (ttt-90) cc_final: 0.8396 (ttt-90) REVERT: Y 149 GLU cc_start: 0.6675 (OUTLIER) cc_final: 0.6397 (mp0) REVERT: Y 243 LYS cc_start: 0.8788 (mtpt) cc_final: 0.8114 (mmtm) REVERT: Y 385 ARG cc_start: 0.8286 (mmt90) cc_final: 0.7987 (mmm-85) REVERT: Y 411 LYS cc_start: 0.8263 (mtpp) cc_final: 0.7986 (ttpt) REVERT: Y 431 LEU cc_start: 0.7819 (tp) cc_final: 0.7601 (tm) REVERT: Y 437 ARG cc_start: 0.7620 (mtt-85) cc_final: 0.7250 (mmm-85) REVERT: Y 484 MET cc_start: 0.8276 (tpp) cc_final: 0.8031 (tpt) REVERT: Z 51 ARG cc_start: 0.8888 (ttt90) cc_final: 0.8251 (ttt90) REVERT: Z 82 ASP cc_start: 0.8343 (t0) cc_final: 0.7615 (t0) REVERT: Z 152 GLU cc_start: 0.8616 (tp30) cc_final: 0.8390 (mm-30) REVERT: Z 292 GLN cc_start: 0.8259 (tt0) cc_final: 0.7920 (tt0) REVERT: Z 411 LYS cc_start: 0.7987 (tmmt) cc_final: 0.7474 (mptp) REVERT: Z 484 MET cc_start: 0.7140 (mmm) cc_final: 0.6428 (tpp) REVERT: Z 493 LYS cc_start: 0.7578 (mtmt) cc_final: 0.7287 (mttt) REVERT: Z 535 LYS cc_start: 0.7796 (mtpt) cc_final: 0.6881 (mmmt) outliers start: 106 outliers final: 62 residues processed: 498 average time/residue: 0.6026 time to fit residues: 366.0901 Evaluate side-chains 485 residues out of total 3569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 406 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain H residue 95 ILE Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 92 ASN Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain P residue 136 GLU Chi-restraints excluded: chain R residue 35 GLU Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 126 LYS Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 86 VAL Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 232 ASP Chi-restraints excluded: chain S residue 266 GLU Chi-restraints excluded: chain S residue 275 GLU Chi-restraints excluded: chain T residue 103 VAL Chi-restraints excluded: chain T residue 183 SER Chi-restraints excluded: chain T residue 279 THR Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 198 VAL Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 149 GLN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 427 VAL Chi-restraints excluded: chain V residue 442 VAL Chi-restraints excluded: chain V residue 448 LEU Chi-restraints excluded: chain V residue 465 ASP Chi-restraints excluded: chain V residue 515 GLN Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 415 ASP Chi-restraints excluded: chain X residue 430 LYS Chi-restraints excluded: chain X residue 435 ARG Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 468 SER Chi-restraints excluded: chain Y residue 149 GLU Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Z residue 69 SER Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain Z residue 426 SER Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 528 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: [147, 308, 167, 363, 129, 365, 49, 341, 249, 133, 309] chunk 147 optimal weight: 0.8980 chunk 308 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 chunk 363 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 365 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 341 optimal weight: 2.9990 chunk 249 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 309 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 98 GLN J 92 ASN ** Q 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 169 GLN ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 529 ASN U 539 ASN V 471 GLN V 515 GLN Y 83 ASN ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.144729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.101158 restraints weight = 44842.222| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.61 r_work: 0.3060 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34443 Z= 0.146 Angle : 0.587 11.527 46679 Z= 0.294 Chirality : 0.045 0.276 5526 Planarity : 0.004 0.053 5999 Dihedral : 5.515 102.250 4827 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.67 % Favored : 96.30 % Rotamer: Outliers : 2.61 % Allowed : 21.05 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.13), residues: 4463 helix: 0.37 (0.11), residues: 2207 sheet: -0.47 (0.22), residues: 567 loop : -0.43 (0.16), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG T 199 TYR 0.018 0.001 TYR T 502 PHE 0.032 0.002 PHE H 107 TRP 0.010 0.001 TRP R 37 HIS 0.003 0.001 HIS S 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (34443) covalent geometry : angle 0.58656 / 0.29 (46679) hydrogen bonds : bond 0.03477 / 2.30 ( 1596) hydrogen bonds : angle 4.47454 / 3.08 ( 4593) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8926 Ramachandran restraints generated. 4463 Oldfield, 0 Emsley, 4463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 418 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.7809 (tm) cc_final: 0.7512 (tt) REVERT: B 82 PHE cc_start: 0.8279 (m-80) cc_final: 0.7839 (m-10) REVERT: C 69 ILE cc_start: 0.8203 (pt) cc_final: 0.7862 (pp) REVERT: C 81 MET cc_start: 0.8015 (tpp) cc_final: 0.7447 (ttm) REVERT: D 61 MET cc_start: 0.7952 (mpt) cc_final: 0.7728 (mmt) REVERT: E 109 LEU cc_start: 0.7916 (tp) cc_final: 0.7658 (tp) REVERT: G 62 VAL cc_start: 0.7624 (OUTLIER) cc_final: 0.7421 (p) REVERT: G 102 TYR cc_start: 0.7202 (m-10) cc_final: 0.6806 (m-80) REVERT: I 98 GLN cc_start: 0.7587 (tm-30) cc_final: 0.7332 (tm-30) REVERT: I 99 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6471 (mp) REVERT: I 119 LEU cc_start: 0.6650 (OUTLIER) cc_final: 0.6383 (pp) REVERT: J 61 MET cc_start: 0.7573 (mpt) cc_final: 0.7202 (mpm) REVERT: J 66 CYS cc_start: 0.8159 (m) cc_final: 0.7707 (m) REVERT: J 107 PHE cc_start: 0.6768 (t80) cc_final: 0.6216 (t80) REVERT: P 49 THR cc_start: 0.8385 (OUTLIER) cc_final: 0.8105 (t) REVERT: P 63 LYS cc_start: 0.8731 (tppt) cc_final: 0.8485 (tptm) REVERT: P 72 ASP cc_start: 0.7830 (t0) cc_final: 0.7238 (t70) REVERT: P 122 PHE cc_start: 0.8681 (m-80) cc_final: 0.8318 (m-80) REVERT: P 134 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8611 (tp) REVERT: P 136 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8218 (tp30) REVERT: Q 10 ARG cc_start: 0.7744 (tpp-160) cc_final: 0.7197 (ttm-80) REVERT: Q 21 ASN cc_start: 0.8623 (m-40) cc_final: 0.8237 (m110) REVERT: Q 40 GLN cc_start: 0.7139 (mm-40) cc_final: 0.6807 (tp-100) REVERT: R 35 GLU cc_start: 0.6707 (OUTLIER) cc_final: 0.6207 (mm-30) REVERT: S 190 TYR cc_start: 0.8404 (m-80) cc_final: 0.8067 (m-80) REVERT: S 203 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.7804 (m-80) REVERT: S 232 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7612 (m-30) REVERT: S 234 GLU cc_start: 0.8047 (tm-30) cc_final: 0.6854 (tm-30) REVERT: S 266 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8643 (tt0) REVERT: S 275 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7710 (tm-30) REVERT: T 447 LYS cc_start: 0.7954 (ptpt) cc_final: 0.7724 (ptpp) REVERT: U 71 LYS cc_start: 0.8380 (tppt) cc_final: 0.8070 (tppp) REVERT: U 84 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8958 (mp) REVERT: V 67 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8325 (mt) REVERT: V 134 ASN cc_start: 0.8527 (p0) cc_final: 0.8076 (t0) REVERT: V 149 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7764 (mm-40) REVERT: V 455 GLU cc_start: 0.8013 (pt0) cc_final: 0.7623 (pp20) REVERT: X 430 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8039 (ttmt) REVERT: Y 51 ARG cc_start: 0.8773 (ttt-90) cc_final: 0.8403 (ttt-90) REVERT: Y 149 GLU cc_start: 0.6706 (OUTLIER) cc_final: 0.6440 (mp0) REVERT: Y 243 LYS cc_start: 0.8798 (mtpt) cc_final: 0.8148 (mmtm) REVERT: Y 385 ARG cc_start: 0.8292 (mmt90) cc_final: 0.7998 (mmm-85) REVERT: Y 411 LYS cc_start: 0.8323 (mtpp) cc_final: 0.8042 (ttpt) REVERT: Y 431 LEU cc_start: 0.7876 (tp) cc_final: 0.7660 (tm) REVERT: Y 437 ARG cc_start: 0.7695 (mtt-85) cc_final: 0.7351 (mmm-85) REVERT: Y 484 MET cc_start: 0.8299 (tpp) cc_final: 0.8001 (tpt) REVERT: Z 82 ASP cc_start: 0.8346 (t0) cc_final: 0.8078 (t0) REVERT: Z 152 GLU cc_start: 0.8607 (tp30) cc_final: 0.8388 (mm-30) REVERT: Z 292 GLN cc_start: 0.8298 (tt0) cc_final: 0.7971 (tt0) REVERT: Z 411 LYS cc_start: 0.7998 (tmmt) cc_final: 0.7501 (mptp) REVERT: Z 484 MET cc_start: 0.7300 (mmm) cc_final: 0.6590 (tpp) REVERT: Z 493 LYS cc_start: 0.7632 (mtmt) cc_final: 0.7259 (mttt) REVERT: Z 535 LYS cc_start: 0.7761 (mtpt) cc_final: 0.6845 (mmmt) outliers start: 93 outliers final: 56 residues processed: 483 average time/residue: 0.6054 time to fit residues: 357.8466 Evaluate side-chains 484 residues out of total 3569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 412 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain H residue 95 ILE Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain P residue 136 GLU Chi-restraints excluded: chain R residue 35 GLU Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 126 LYS Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 86 VAL Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 232 ASP Chi-restraints excluded: chain S residue 266 GLU Chi-restraints excluded: chain S residue 275 GLU Chi-restraints excluded: chain T residue 103 VAL Chi-restraints excluded: chain T residue 183 SER Chi-restraints excluded: chain T residue 279 THR Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 198 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 149 GLN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 427 VAL Chi-restraints excluded: chain V residue 442 VAL Chi-restraints excluded: chain V residue 448 LEU Chi-restraints excluded: chain V residue 465 ASP Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 415 ASP Chi-restraints excluded: chain X residue 430 LYS Chi-restraints excluded: chain X residue 435 ARG Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 468 SER Chi-restraints excluded: chain Y residue 149 GLU Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Z residue 69 SER Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain Z residue 426 SER Chi-restraints excluded: chain Z residue 456 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: [67, 254, 56, 94, 82, 234, 386, 430, 387, 166, 22] chunk 67 optimal weight: 0.3980 chunk 254 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 234 optimal weight: 0.6980 chunk 386 optimal weight: 8.9990 chunk 430 optimal weight: 0.8980 chunk 387 optimal weight: 0.8980 chunk 166 optimal weight: 0.2980 chunk 22 optimal weight: 8.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 98 GLN J 98 GLN ** Q 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 169 GLN ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 529 ASN U 539 ASN V 471 GLN Y 83 ASN ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 440 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.145657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.102266 restraints weight = 44587.917| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.61 r_work: 0.3047 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34443 Z= 0.127 Angle : 0.572 10.911 46679 Z= 0.287 Chirality : 0.044 0.280 5526 Planarity : 0.004 0.052 5999 Dihedral : 5.424 102.775 4827 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.45 % Favored : 96.53 % Rotamer: Outliers : 2.41 % Allowed : 21.52 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.13), residues: 4463 helix: 0.50 (0.11), residues: 2201 sheet: -0.47 (0.22), residues: 567 loop : -0.42 (0.16), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG T 199 TYR 0.016 0.001 TYR T 502 PHE 0.035 0.002 PHE B 107 TRP 0.008 0.001 TRP R 37 HIS 0.003 0.001 HIS U 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (34443) covalent geometry : angle 0.57248 / 0.29 (46679) hydrogen bonds : bond 0.03309 / 2.19 ( 1596) hydrogen bonds : angle 4.41842 / 3.04 ( 4593) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13892.14 seconds wall clock time: 236 minutes 28.46 seconds (14188.46 seconds total)